Starting phenix.real_space_refine on Sun Feb 8 08:28:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nvu_12613/02_2026/7nvu_12613.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nvu_12613/02_2026/7nvu_12613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nvu_12613/02_2026/7nvu_12613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nvu_12613/02_2026/7nvu_12613.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nvu_12613/02_2026/7nvu_12613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nvu_12613/02_2026/7nvu_12613.map" } resolution = 2.5 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= -0.001 sd= 0.981 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 89 5.49 5 Mg 1 5.21 5 S 250 5.16 5 C 27644 2.51 5 N 7777 2.21 5 O 8469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44240 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 11274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1423, 11274 Classifications: {'peptide': 1423} Link IDs: {'PCIS': 3, 'PTRANS': 67, 'TRANS': 1352} Chain breaks: 4 Chain: "B" Number of atoms: 9076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 9076 Classifications: {'peptide': 1136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1082} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 928 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2301 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 15, 'TRANS': 282} Chain breaks: 1 Chain: "N" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 914 Classifications: {'DNA': 44} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 43} Chain breaks: 1 Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1422 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "Q" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Chain: "T" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 911 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 14 Chain: "U" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 930 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "V" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "W" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1535 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 5, 'TRANS': 181} Chain: "X" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" 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 464 SG CYS A 71 100.911 106.992 67.692 1.00 31.19 S ATOM 486 SG CYS A 74 99.467 105.949 64.422 1.00 39.86 S ATOM 533 SG CYS A 81 98.849 103.875 67.448 1.00 31.84 S ATOM 768 SG CYS A 111 138.084 78.462 71.813 1.00 64.47 S ATOM 796 SG CYS A 114 140.458 79.737 68.929 1.00 67.75 S ATOM 1109 SG CYS A 154 140.282 76.135 70.096 1.00 79.92 S ATOM 1132 SG CYS A 184 141.931 79.216 71.878 1.00 79.38 S ATOM 19919 SG CYS B1119 110.251 97.095 54.840 1.00 19.77 S ATOM 19941 SG CYS B1122 111.263 95.500 58.096 1.00 31.20 S ATOM 20056 SG CYS B1137 110.702 99.189 57.888 1.00 43.68 S ATOM 20077 SG CYS B1140 113.667 97.579 56.240 1.00 49.84 S ATOM 21044 SG CYS C 88 32.361 101.033 72.561 1.00 30.76 S ATOM 21057 SG CYS C 90 34.820 103.254 74.541 1.00 50.98 S ATOM 21092 SG CYS C 94 31.599 102.667 75.813 1.00 25.33 S ATOM 21114 SG CYS C 97 33.997 99.818 75.736 1.00 23.56 S ATOM 28400 SG CYS I 17 126.950 42.135 122.346 1.00 76.73 S ATOM 28424 SG CYS I 20 127.498 45.607 121.885 1.00 83.36 S ATOM 28585 SG CYS I 39 128.475 43.197 119.089 1.00 81.10 S ATOM 28610 SG CYS I 42 130.632 43.490 122.847 1.00 88.26 S ATOM 28962 SG CYS I 86 87.063 23.293 121.178 1.00 60.43 S ATOM 28986 SG CYS I 89 85.070 23.587 124.372 1.00 76.35 S ATOM 29190 SG CYS I 114 85.182 26.465 122.059 1.00 48.41 S ATOM 29225 SG CYS I 119 88.194 25.465 124.030 1.00 63.36 S ATOM 29336 SG CYS J 7 41.192 72.302 89.249 1.00 20.68 S ATOM 29360 SG CYS J 10 37.931 72.015 87.279 1.00 20.68 S ATOM 29624 SG CYS J 44 40.022 68.921 88.245 1.00 2.84 S ATOM 29630 SG CYS J 45 37.936 70.875 90.592 1.00 20.68 S ATOM 30750 SG CYS L 19 61.822 104.384 110.330 1.00 31.60 S ATOM 30769 SG CYS L 22 59.069 105.930 112.350 1.00 38.25 S ATOM 30886 SG CYS L 36 61.809 107.960 111.287 1.00 31.17 S ATOM 30912 SG CYS L 39 62.486 105.398 113.802 1.00 47.93 S ATOM 31094 SG CYS M 15 76.406 113.441 60.741 1.00 62.91 S ATOM 31241 SG CYS M 34 74.000 113.311 63.603 1.00 46.82 S ATOM 31263 SG CYS M 37 73.119 111.798 60.162 1.00 54.45 S ATOM 42289 SG CYS W 129 109.279 131.113 59.019 1.00113.62 S ATOM 42481 SG CYS W 154 105.723 128.779 58.778 1.00114.80 S ATOM 42505 SG CYS W 157 105.767 131.602 60.984 1.00112.77 S Time building chain proxies: 9.20, per 1000 atoms: 0.21 Number of scatterers: 44240 At special positions: 0 Unit cell: (175.35, 171.15, 182.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 250 16.00 P 89 15.00 Mg 1 11.99 O 8469 8.00 N 7777 7.00 C 27644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" NE2 HIS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 37 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 34 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 15 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 157 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 154 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 129 " Number of angles added : 48 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9990 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 0 sheets defined 36.0% alpha, 0.0% beta 38 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 5.19 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 Processing helix chain 'A' and resid 97 through 109 removed outlier: 4.673A pdb=" N VAL A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LYS A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.534A pdb=" N THR A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 227 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 245 through 248 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 275 through 296 Processing helix chain 'A' and resid 300 through 318 removed outlier: 3.631A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 435 through 438 No H-bonds generated for 'chain 'A' and resid 435 through 438' Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.588A pdb=" N THR A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) Proline residue: A 491 - end of helix No H-bonds generated for 'chain 'A' and resid 487 through 492' Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 521 through 524 Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 557 through 566 removed outlier: 3.909A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 Processing helix chain 'A' and resid 611 through 613 No H-bonds generated for 'chain 'A' and resid 611 through 613' Processing helix chain 'A' and resid 642 through 645 No H-bonds generated for 'chain 'A' and resid 642 through 645' Processing helix chain 'A' and resid 652 through 660 Processing helix chain 'A' and resid 662 through 683 removed outlier: 4.112A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 692 Processing helix chain 'A' and resid 696 through 721 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 765 through 771 Processing helix chain 'A' and resid 778 through 785 Processing helix chain 'A' and resid 833 through 868 removed outlier: 3.534A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 913 through 920 Processing helix chain 'A' and resid 927 through 933 Processing helix chain 'A' and resid 936 through 944 removed outlier: 3.934A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 969 Processing helix chain 'A' and resid 983 through 993 Processing helix chain 'A' and resid 1006 through 1019 Processing helix chain 'A' and resid 1028 through 1037 Processing helix chain 'A' and resid 1039 through 1048 Processing helix chain 'A' and resid 1051 through 1056 Processing helix chain 'A' and resid 1062 through 1079 Processing helix chain 'A' and resid 1087 through 1101 Proline residue: A1098 - end of helix removed outlier: 4.144A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1128 Processing helix chain 'A' and resid 1151 through 1161 removed outlier: 3.578A pdb=" N ILE A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1198 removed outlier: 4.353A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1224 Processing helix chain 'A' and resid 1228 through 1239 Processing helix chain 'A' and resid 1263 through 1266 No H-bonds generated for 'chain 'A' and resid 1263 through 1266' Processing helix chain 'A' and resid 1283 through 1294 Processing helix chain 'A' and resid 1343 through 1348 removed outlier: 3.521A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1369 Processing helix chain 'A' and resid 1371 through 1389 removed outlier: 4.804A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1406 Processing helix chain 'A' and resid 1416 through 1419 No H-bonds generated for 'chain 'A' and resid 1416 through 1419' Processing helix chain 'A' and resid 1426 through 1432 Processing helix chain 'A' and resid 1435 through 1444 Processing helix chain 'A' and resid 1454 through 1459 Processing helix chain 'A' and resid 1467 through 1469 No H-bonds generated for 'chain 'A' and resid 1467 through 1469' Processing helix chain 'A' and resid 1477 through 1481 Processing helix chain 'B' and resid 19 through 37 removed outlier: 4.461A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 110 through 116 Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 281 through 288 Processing helix chain 'B' and resid 295 through 307 removed outlier: 3.530A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 314 through 324 removed outlier: 3.805A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 345 Processing helix chain 'B' and resid 358 through 377 Processing helix chain 'B' and resid 396 through 424 removed outlier: 3.629A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 496 through 499 No H-bonds generated for 'chain 'B' and resid 496 through 499' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 539 through 547 Processing helix chain 'B' and resid 558 through 561 Processing helix chain 'B' and resid 580 through 593 Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.618A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 672' Processing helix chain 'B' and resid 679 through 682 No H-bonds generated for 'chain 'B' and resid 679 through 682' Processing helix chain 'B' and resid 700 through 703 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 719 through 731 removed outlier: 3.739A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 765 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 975 Proline residue: B 973 - end of helix Processing helix chain 'B' and resid 978 through 993 Processing helix chain 'B' and resid 1008 through 1018 removed outlier: 3.581A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1057 No H-bonds generated for 'chain 'B' and resid 1055 through 1057' Processing helix chain 'B' and resid 1088 through 1097 Processing helix chain 'B' and resid 1100 through 1107 Processing helix chain 'B' and resid 1153 through 1165 Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 61 through 70 Processing helix chain 'C' and resid 78 through 81 No H-bonds generated for 'chain 'C' and resid 78 through 81' Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 241 through 270 Processing helix chain 'D' and resid 34 through 49 Processing helix chain 'D' and resid 59 through 71 Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 124 through 137 Processing helix chain 'E' and resid 3 through 23 Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 44 Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 112 through 120 removed outlier: 3.711A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 153 through 163 Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 74 Processing helix chain 'F' and resid 89 through 99 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'H' and resid 84 through 87 Processing helix chain 'H' and resid 129 through 132 Processing helix chain 'I' and resid 64 through 67 No H-bonds generated for 'chain 'I' and resid 64 through 67' Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 31 through 37 Processing helix chain 'J' and resid 43 through 50 Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.635A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 9 removed outlier: 3.538A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 9' Processing helix chain 'K' and resid 40 through 52 removed outlier: 3.734A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 114 Processing helix chain 'M' and resid 90 through 92 No H-bonds generated for 'chain 'M' and resid 90 through 92' Processing helix chain 'M' and resid 109 through 127 Processing helix chain 'M' and resid 132 through 148 Processing helix chain 'M' and resid 156 through 170 Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 188 through 202 Processing helix chain 'M' and resid 211 through 213 No H-bonds generated for 'chain 'M' and resid 211 through 213' Processing helix chain 'M' and resid 215 through 222 Processing helix chain 'M' and resid 226 through 242 Processing helix chain 'M' and resid 250 through 263 Processing helix chain 'M' and resid 271 through 278 Processing helix chain 'M' and resid 282 through 293 Processing helix chain 'M' and resid 296 through 299 No H-bonds generated for 'chain 'M' and resid 296 through 299' Processing helix chain 'M' and resid 310 through 312 No H-bonds generated for 'chain 'M' and resid 310 through 312' Processing helix chain 'O' and resid 180 through 186 Processing helix chain 'O' and resid 227 through 244 Processing helix chain 'O' and resid 270 through 276 Processing helix chain 'O' and resid 318 through 335 Proline residue: O 330 - end of helix removed outlier: 3.627A pdb=" N PHE O 335 " --> pdb=" O ILE O 331 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 9 Processing helix chain 'Q' and resid 33 through 35 No H-bonds generated for 'chain 'Q' and resid 33 through 35' Processing helix chain 'Q' and resid 157 through 165 removed outlier: 3.820A pdb=" N GLU Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU Q 165 " --> pdb=" O GLU Q 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 179 removed outlier: 4.481A pdb=" N MET Q 177 " --> pdb=" O HIS Q 173 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN Q 178 " --> pdb=" O PHE Q 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 13 No H-bonds generated for 'chain 'R' and resid 10 through 13' Processing helix chain 'R' and resid 25 through 34 Processing helix chain 'R' and resid 60 through 63 No H-bonds generated for 'chain 'R' and resid 60 through 63' Processing helix chain 'R' and resid 123 through 137 removed outlier: 3.788A pdb=" N LEU R 127 " --> pdb=" O ASN R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 172 Processing helix chain 'R' and resid 180 through 193 removed outlier: 3.848A pdb=" N LYS R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 206 removed outlier: 3.786A pdb=" N ASP R 204 " --> pdb=" O LYS R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 220 removed outlier: 3.687A pdb=" N ILE R 220 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 31 removed outlier: 4.459A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 50 removed outlier: 3.553A pdb=" N LYS U 49 " --> pdb=" O TRP U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 325 through 329 Processing helix chain 'V' and resid 6 through 8 No H-bonds generated for 'chain 'V' and resid 6 through 8' Processing helix chain 'V' and resid 10 through 24 Processing helix chain 'V' and resid 30 through 51 Processing helix chain 'W' and resid 12 through 25 Processing helix chain 'W' and resid 28 through 39 Processing helix chain 'W' and resid 45 through 52 Processing helix chain 'W' and resid 56 through 69 Processing helix chain 'W' and resid 96 through 123 removed outlier: 3.626A pdb=" N ASN W 101 " --> pdb=" O ARG W 97 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG W 119 " --> pdb=" O GLU W 115 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR W 122 " --> pdb=" O GLU W 118 " (cutoff:3.500A) Processing helix chain 'W' and resid 138 through 144 Processing helix chain 'W' and resid 164 through 183 removed outlier: 3.856A pdb=" N MET W 168 " --> pdb=" O ASP W 164 " (cutoff:3.500A) Proline residue: W 169 - end of helix removed outlier: 3.751A pdb=" N ASP W 172 " --> pdb=" O MET W 168 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA W 173 " --> pdb=" O PRO W 169 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG W 174 " --> pdb=" O LYS W 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR W 175 " --> pdb=" O LYS W 171 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA W 178 " --> pdb=" O ARG W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 185 through 194 Processing helix chain 'X' and resid 77 through 90 Processing helix chain 'X' and resid 99 through 105 removed outlier: 3.670A pdb=" N GLU X 105 " --> pdb=" O GLU X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 121 Processing helix chain 'X' and resid 123 through 126 No H-bonds generated for 'chain 'X' and resid 123 through 126' Processing helix chain 'X' and resid 148 through 161 Processing helix chain 'X' and resid 168 through 174 Processing helix chain 'X' and resid 178 through 188 removed outlier: 5.967A pdb=" N ASP X 187 " --> pdb=" O LYS X 183 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLN X 188 " --> pdb=" O ALA X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 214 through 222 Processing helix chain 'X' and resid 230 through 240 removed outlier: 3.870A pdb=" N LEU X 237 " --> pdb=" O ILE X 233 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS X 238 " --> pdb=" O GLU X 234 " (cutoff:3.500A) 1098 hydrogen bonds defined for protein. 3225 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 206 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 7.12 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14384 1.34 - 1.46: 7419 1.46 - 1.58: 22859 1.58 - 1.70: 175 1.70 - 1.82: 394 Bond restraints: 45231 Sorted by residual: bond pdb=" N MET V 1 " pdb=" CA MET V 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N MET K 1 " pdb=" CA MET K 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.64e+00 bond pdb=" CB TRP B 453 " pdb=" CG TRP B 453 " ideal model delta sigma weight residual 1.498 1.456 0.042 3.10e-02 1.04e+03 1.83e+00 ... (remaining 45226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 60524 1.43 - 2.86: 665 2.86 - 4.29: 235 4.29 - 5.72: 9 5.72 - 7.15: 1 Bond angle restraints: 61434 Sorted by residual: angle pdb=" CG ARG A 483 " pdb=" CD ARG A 483 " pdb=" NE ARG A 483 " ideal model delta sigma weight residual 112.00 119.15 -7.15 2.20e+00 2.07e-01 1.06e+01 angle pdb=" N GLY B 150 " pdb=" CA GLY B 150 " pdb=" C GLY B 150 " ideal model delta sigma weight residual 110.46 114.09 -3.63 1.43e+00 4.89e-01 6.44e+00 angle pdb=" N ILE A 682 " pdb=" CA ILE A 682 " pdb=" C ILE A 682 " ideal model delta sigma weight residual 111.45 109.11 2.34 9.30e-01 1.16e+00 6.36e+00 angle pdb=" N ARG O 205 " pdb=" CA ARG O 205 " pdb=" C ARG O 205 " ideal model delta sigma weight residual 111.36 113.97 -2.61 1.09e+00 8.42e-01 5.74e+00 angle pdb=" C3' DA T -34 " pdb=" C2' DA T -34 " pdb=" C1' DA T -34 " ideal model delta sigma weight residual 101.60 105.19 -3.59 1.50e+00 4.44e-01 5.74e+00 ... (remaining 61429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 24472 17.97 - 35.94: 2279 35.94 - 53.90: 524 53.90 - 71.87: 159 71.87 - 89.84: 55 Dihedral angle restraints: 27489 sinusoidal: 12064 harmonic: 15425 Sorted by residual: dihedral pdb=" CA VAL A 538 " pdb=" C VAL A 538 " pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta harmonic sigma weight residual -180.00 -145.82 -34.18 0 5.00e+00 4.00e-02 4.67e+01 dihedral pdb=" CA LYS O 297 " pdb=" C LYS O 297 " pdb=" N PRO O 298 " pdb=" CA PRO O 298 " ideal model delta harmonic sigma weight residual 180.00 154.25 25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ASN A1129 " pdb=" C ASN A1129 " pdb=" N ILE A1130 " pdb=" CA ILE A1130 " ideal model delta harmonic sigma weight residual -180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 27486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 4335 0.028 - 0.057: 1573 0.057 - 0.085: 443 0.085 - 0.113: 393 0.113 - 0.141: 105 Chirality restraints: 6849 Sorted by residual: chirality pdb=" CA ILE A 419 " pdb=" N ILE A 419 " pdb=" C ILE A 419 " pdb=" CB ILE A 419 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE J 3 " pdb=" N ILE J 3 " pdb=" C ILE J 3 " pdb=" CB ILE J 3 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA PRO B1001 " pdb=" N PRO B1001 " pdb=" C PRO B1001 " pdb=" CB PRO B1001 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 6846 not shown) Planarity restraints: 7660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B1048 " 0.018 2.00e-02 2.50e+03 1.77e-02 6.24e+00 pdb=" CG TYR B1048 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR B1048 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B1048 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B1048 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B1048 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B1048 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B1048 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS O 297 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO O 298 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO O 298 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO O 298 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1168 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO B1169 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B1169 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B1169 " -0.027 5.00e-02 4.00e+02 ... (remaining 7657 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 216 2.49 - 3.09: 32437 3.09 - 3.70: 70752 3.70 - 4.30: 108665 4.30 - 4.90: 172328 Nonbonded interactions: 384398 Sorted by model distance: nonbonded pdb=" OD2 ASP H 8 " pdb=" OG SER H 32 " model vdw 1.889 3.040 nonbonded pdb=" NH2 ARG C 67 " pdb=" O ILE J 3 " model vdw 1.900 3.120 nonbonded pdb=" OD2 ASP E 3 " pdb=" OG SER E 49 " model vdw 2.008 3.040 nonbonded pdb=" O MET A 535 " pdb=" OH TYR A 669 " model vdw 2.022 3.040 nonbonded pdb=" OG1 THR B 474 " pdb=" O ALA B 732 " model vdw 2.038 3.040 ... (remaining 384393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.960 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: 0.040 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 44.940 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 : 0.004 0.225 45270 Z= 0.155 Angle : 0.472 15.286 61482 Z= 0.263 Chirality : 0.040 0.141 6849 Planarity : 0.003 0.054 7660 Dihedral : 15.453 89.841 17499 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.12), residues: 5233 helix: 1.96 (0.12), residues: 1939 sheet: 0.62 (0.18), residues: 851 loop : 0.33 (0.13), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 483 TYR 0.043 0.001 TYR B1048 PHE 0.032 0.001 PHE A 458 TRP 0.012 0.001 TRP C 203 HIS 0.007 0.001 HIS M 18 Details of bonding type rmsd covalent geometry : bond 0.00296 (45231) covalent geometry : angle 0.45439 (61434) hydrogen bonds : bond 0.21242 ( 1201) hydrogen bonds : angle 5.82471 ( 3431) metal coordination : bond 0.07387 ( 39) metal coordination : angle 4.65463 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 918 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7804 (mmt90) cc_final: 0.7559 (mpt-90) REVERT: A 220 ARG cc_start: 0.8257 (tpt-90) cc_final: 0.7750 (tpt170) REVERT: A 439 HIS cc_start: 0.7424 (t70) cc_final: 0.7136 (m-70) REVERT: A 845 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7491 (mm-30) REVERT: A 1306 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7737 (tppt) REVERT: A 1472 ASP cc_start: 0.7669 (m-30) cc_final: 0.7420 (m-30) REVERT: B 677 MET cc_start: 0.9008 (tpp) cc_final: 0.8562 (tpp) REVERT: B 1104 ARG cc_start: 0.8580 (ttt-90) cc_final: 0.8315 (ttp-170) REVERT: E 23 ASP cc_start: 0.8168 (m-30) cc_final: 0.7953 (m-30) REVERT: E 116 GLN cc_start: 0.8295 (tp40) cc_final: 0.7833 (tp40) REVERT: E 137 ILE cc_start: 0.8499 (pt) cc_final: 0.8277 (pt) REVERT: F 59 LYS cc_start: 0.9136 (ptpt) cc_final: 0.8905 (ptmt) REVERT: G 117 MET cc_start: -0.0139 (mmm) cc_final: -0.0980 (tmm) REVERT: H 111 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7672 (mtp-110) REVERT: H 123 MET cc_start: 0.8966 (ttp) cc_final: 0.8718 (ttp) REVERT: I 34 ILE cc_start: 0.8278 (tp) cc_final: 0.8032 (pp) REVERT: I 37 TYR cc_start: 0.8607 (m-80) cc_final: 0.8401 (m-80) REVERT: I 56 ASN cc_start: 0.8679 (t0) cc_final: 0.8349 (t0) REVERT: L 58 ARG cc_start: 0.7867 (mtt180) cc_final: 0.7601 (mtt180) REVERT: M 52 TRP cc_start: 0.8354 (p90) cc_final: 0.8009 (p90) REVERT: M 86 LYS cc_start: 0.7711 (mttt) cc_final: 0.7433 (ttpp) REVERT: M 190 GLU cc_start: 0.7639 (tp30) cc_final: 0.7364 (tp30) REVERT: M 300 PHE cc_start: 0.8196 (m-80) cc_final: 0.7876 (m-80) REVERT: O 277 HIS cc_start: 0.8618 (m-70) cc_final: 0.8369 (m90) REVERT: Q 111 LYS cc_start: 0.8259 (ttpt) cc_final: 0.7926 (tptt) outliers start: 0 outliers final: 1 residues processed: 918 average time/residue: 0.8853 time to fit residues: 967.1227 Evaluate side-chains 633 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 632 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 130 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 394 optimal weight: 0.6980 chunk 430 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 265 optimal weight: 0.0770 chunk 523 optimal weight: 7.9990 chunk 497 optimal weight: 3.9990 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 30.0000 chunk 366 optimal weight: 0.9990 chunk 223 optimal weight: 0.0000 overall best weight: 0.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 459 ASN A 711 GLN A 722 ASN A 861 GLN A1077 ASN A1299 GLN ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN B 585 ASN B 649 ASN B 968 ASN B1117 HIS C 18 ASN C 111 GLN C 217 GLN E 92 GLN H 76 ASN K 89 ASN ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 ASN O 277 HIS O 327 ASN Q 168 ASN R 144 GLN ** W 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.205845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.132518 restraints weight = 47094.158| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.75 r_work: 0.3041 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 45270 Z= 0.151 Angle : 0.568 17.068 61482 Z= 0.290 Chirality : 0.043 0.235 6849 Planarity : 0.004 0.058 7660 Dihedral : 11.929 59.872 6736 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.81 % Allowed : 9.95 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.12), residues: 5233 helix: 1.55 (0.12), residues: 1964 sheet: 0.63 (0.18), residues: 861 loop : 0.20 (0.13), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1258 TYR 0.021 0.001 TYR A1482 PHE 0.028 0.002 PHE A 458 TRP 0.015 0.001 TRP C 203 HIS 0.010 0.001 HIS M 18 Details of bonding type rmsd covalent geometry : bond 0.00339 (45231) covalent geometry : angle 0.55014 (61434) hydrogen bonds : bond 0.05022 ( 1201) hydrogen bonds : angle 4.07720 ( 3431) metal coordination : bond 0.01964 ( 39) metal coordination : angle 5.14681 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 671 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8495 (mmt90) cc_final: 0.8251 (mpt-90) REVERT: A 67 ARG cc_start: 0.7913 (mmm160) cc_final: 0.6957 (mmm160) REVERT: A 108 ARG cc_start: 0.8864 (mtt180) cc_final: 0.8653 (mtt180) REVERT: A 220 ARG cc_start: 0.8589 (tpt-90) cc_final: 0.7676 (tpm-80) REVERT: A 296 ASN cc_start: 0.7501 (m-40) cc_final: 0.7266 (m110) REVERT: A 423 ASN cc_start: 0.7653 (p0) cc_final: 0.7303 (p0) REVERT: A 425 ASP cc_start: 0.8124 (m-30) cc_final: 0.7769 (m-30) REVERT: A 439 HIS cc_start: 0.7450 (t70) cc_final: 0.7014 (m-70) REVERT: A 708 LYS cc_start: 0.8300 (mppt) cc_final: 0.8090 (mptt) REVERT: A 715 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: A 928 ARG cc_start: 0.7438 (mtp85) cc_final: 0.7147 (mtp85) REVERT: A 1155 LYS cc_start: 0.7659 (ttpt) cc_final: 0.7201 (tttm) REVERT: A 1162 GLU cc_start: 0.8392 (tt0) cc_final: 0.8005 (tt0) REVERT: A 1219 LYS cc_start: 0.8193 (tppt) cc_final: 0.7897 (tppt) REVERT: A 1244 ASN cc_start: 0.8097 (t0) cc_final: 0.7854 (m110) REVERT: A 1288 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8635 (mp) REVERT: A 1306 LYS cc_start: 0.8392 (ttmm) cc_final: 0.7791 (tppt) REVERT: A 1437 ASP cc_start: 0.8105 (m-30) cc_final: 0.7861 (m-30) REVERT: A 1472 ASP cc_start: 0.8551 (m-30) cc_final: 0.8299 (m-30) REVERT: B 24 GLU cc_start: 0.7737 (mp0) cc_final: 0.7393 (tm-30) REVERT: B 143 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8121 (pm20) REVERT: B 287 HIS cc_start: 0.8615 (m90) cc_final: 0.8374 (m170) REVERT: B 291 ASP cc_start: 0.8016 (t0) cc_final: 0.7691 (t0) REVERT: B 582 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8023 (tm130) REVERT: B 731 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8598 (mt0) REVERT: B 1081 ASP cc_start: 0.6711 (t0) cc_final: 0.6387 (t0) REVERT: B 1104 ARG cc_start: 0.9120 (ttt-90) cc_final: 0.8802 (ttp-170) REVERT: B 1127 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8427 (mt) REVERT: C 27 ASP cc_start: 0.8150 (t70) cc_final: 0.7864 (t0) REVERT: C 86 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7244 (ptt90) REVERT: E 41 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7753 (mmtt) REVERT: E 87 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8644 (mt) REVERT: E 92 GLN cc_start: 0.8491 (tp40) cc_final: 0.8184 (tp-100) REVERT: E 116 GLN cc_start: 0.8561 (tp40) cc_final: 0.8207 (tp40) REVERT: E 117 SER cc_start: 0.9189 (t) cc_final: 0.8940 (p) REVERT: E 210 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6747 (tt0) REVERT: F 59 LYS cc_start: 0.9363 (ptpt) cc_final: 0.9067 (ptmt) REVERT: F 86 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7586 (mm-30) REVERT: G 117 MET cc_start: -0.0258 (mmm) cc_final: -0.0635 (tmm) REVERT: H 7 GLU cc_start: 0.8469 (tt0) cc_final: 0.8256 (tt0) REVERT: H 111 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.7845 (mtp-110) REVERT: H 123 MET cc_start: 0.9325 (ttp) cc_final: 0.9061 (ttp) REVERT: H 146 LYS cc_start: 0.8530 (tttp) cc_final: 0.8310 (tttp) REVERT: I 34 ILE cc_start: 0.8083 (tp) cc_final: 0.7857 (pp) REVERT: I 37 TYR cc_start: 0.8674 (m-80) cc_final: 0.8442 (m-80) REVERT: I 56 ASN cc_start: 0.8898 (t0) cc_final: 0.8505 (t0) REVERT: J 1 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7745 (mtp) REVERT: L 37 ARG cc_start: 0.7059 (mmt180) cc_final: 0.6657 (ptp-110) REVERT: L 47 LYS cc_start: 0.8084 (ptmt) cc_final: 0.7777 (ptmm) REVERT: M 52 TRP cc_start: 0.7786 (p90) cc_final: 0.7370 (p90) REVERT: M 86 LYS cc_start: 0.7924 (mttt) cc_final: 0.7078 (mtpp) REVERT: M 190 GLU cc_start: 0.8045 (tp30) cc_final: 0.7643 (tp30) REVERT: M 227 GLN cc_start: 0.7186 (pm20) cc_final: 0.6893 (pm20) REVERT: M 300 PHE cc_start: 0.8096 (m-80) cc_final: 0.7715 (m-80) REVERT: R 170 LYS cc_start: 0.8137 (tmmt) cc_final: 0.7934 (tmmt) REVERT: R 181 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8565 (tp-100) REVERT: R 211 VAL cc_start: 0.8558 (t) cc_final: 0.8312 (p) REVERT: U 358 MET cc_start: 0.7128 (ppp) cc_final: 0.4393 (tmt) REVERT: W 76 MET cc_start: 0.4017 (mmm) cc_final: 0.3416 (mmm) outliers start: 85 outliers final: 28 residues processed: 709 average time/residue: 0.8476 time to fit residues: 720.5239 Evaluate side-chains 659 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 619 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 892 CYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1127 ILE Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain W residue 48 MET Chi-restraints excluded: chain W residue 66 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 156 optimal weight: 0.0670 chunk 522 optimal weight: 50.0000 chunk 206 optimal weight: 1.9990 chunk 358 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 517 optimal weight: 10.0000 chunk 166 optimal weight: 0.6980 chunk 361 optimal weight: 0.9980 chunk 335 optimal weight: 6.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN A 861 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 312 GLN B 552 ASN B 585 ASN B 649 ASN B 968 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN I 46 GLN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.204399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.131001 restraints weight = 46686.318| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.73 r_work: 0.3013 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 45270 Z= 0.202 Angle : 0.584 23.754 61482 Z= 0.293 Chirality : 0.044 0.227 6849 Planarity : 0.004 0.058 7660 Dihedral : 12.138 59.927 6734 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.39 % Allowed : 11.55 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.12), residues: 5233 helix: 1.28 (0.12), residues: 1975 sheet: 0.57 (0.18), residues: 852 loop : 0.12 (0.13), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1149 TYR 0.023 0.002 TYR G 3 PHE 0.024 0.002 PHE A 592 TRP 0.018 0.002 TRP B 27 HIS 0.014 0.001 HIS M 18 Details of bonding type rmsd covalent geometry : bond 0.00470 (45231) covalent geometry : angle 0.56361 (61434) hydrogen bonds : bond 0.04859 ( 1201) hydrogen bonds : angle 3.93293 ( 3431) metal coordination : bond 0.01978 ( 39) metal coordination : angle 5.52983 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 627 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8487 (mmt90) cc_final: 0.8151 (mpt-90) REVERT: A 67 ARG cc_start: 0.7945 (mmm160) cc_final: 0.7114 (mmm160) REVERT: A 108 ARG cc_start: 0.8872 (mtt180) cc_final: 0.8611 (mtt180) REVERT: A 220 ARG cc_start: 0.8556 (tpt-90) cc_final: 0.7623 (tpm-80) REVERT: A 296 ASN cc_start: 0.7707 (m-40) cc_final: 0.7407 (m110) REVERT: A 439 HIS cc_start: 0.7488 (t70) cc_final: 0.7037 (m-70) REVERT: A 708 LYS cc_start: 0.8384 (mppt) cc_final: 0.8112 (mptt) REVERT: A 715 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: A 1071 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8148 (tm-30) REVERT: A 1155 LYS cc_start: 0.7662 (ttpt) cc_final: 0.7217 (tttm) REVERT: A 1162 GLU cc_start: 0.8367 (tt0) cc_final: 0.7990 (tt0) REVERT: A 1219 LYS cc_start: 0.8377 (tppt) cc_final: 0.8033 (tppt) REVERT: A 1288 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8714 (mp) REVERT: A 1306 LYS cc_start: 0.8365 (ttmm) cc_final: 0.7771 (tppt) REVERT: A 1351 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8332 (t0) REVERT: A 1416 ARG cc_start: 0.8782 (ptt90) cc_final: 0.8518 (ptt90) REVERT: A 1472 ASP cc_start: 0.8588 (m-30) cc_final: 0.8346 (m-30) REVERT: B 24 GLU cc_start: 0.7757 (mp0) cc_final: 0.7458 (tm-30) REVERT: B 143 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: B 287 HIS cc_start: 0.8591 (m90) cc_final: 0.8298 (m90) REVERT: B 291 ASP cc_start: 0.8053 (t0) cc_final: 0.7734 (t0) REVERT: B 582 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8327 (tm130) REVERT: B 677 MET cc_start: 0.9176 (tpp) cc_final: 0.8855 (tpt) REVERT: B 731 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8619 (mt0) REVERT: B 1104 ARG cc_start: 0.9155 (ttt-90) cc_final: 0.8843 (ttp-170) REVERT: C 17 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: C 27 ASP cc_start: 0.8324 (t70) cc_final: 0.8101 (t0) REVERT: C 86 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7395 (ptt90) REVERT: E 41 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7799 (mmtt) REVERT: E 92 GLN cc_start: 0.8536 (tp40) cc_final: 0.8182 (tp-100) REVERT: E 116 GLN cc_start: 0.8537 (tp40) cc_final: 0.7970 (tp40) REVERT: E 117 SER cc_start: 0.9186 (t) cc_final: 0.8914 (p) REVERT: E 131 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8375 (mm) REVERT: E 133 GLN cc_start: 0.8373 (tp-100) cc_final: 0.8033 (tp-100) REVERT: E 210 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6856 (tt0) REVERT: F 59 LYS cc_start: 0.9387 (ptpt) cc_final: 0.9091 (ptmt) REVERT: G 44 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.6972 (m-10) REVERT: G 104 MET cc_start: 0.7695 (ptm) cc_final: 0.6809 (ppp) REVERT: H 103 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6881 (pm20) REVERT: H 111 ARG cc_start: 0.8248 (mmm-85) cc_final: 0.7844 (mtp-110) REVERT: H 123 MET cc_start: 0.9375 (ttp) cc_final: 0.9120 (ttp) REVERT: H 146 LYS cc_start: 0.8547 (tttp) cc_final: 0.8345 (tttp) REVERT: I 45 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8522 (mt0) REVERT: I 56 ASN cc_start: 0.8918 (t0) cc_final: 0.8512 (t0) REVERT: L 37 ARG cc_start: 0.7285 (mmt180) cc_final: 0.6766 (ptp-110) REVERT: M 52 TRP cc_start: 0.7757 (p90) cc_final: 0.7328 (p90) REVERT: M 86 LYS cc_start: 0.7916 (mttt) cc_final: 0.7077 (mtpp) REVERT: M 190 GLU cc_start: 0.8075 (tp30) cc_final: 0.7682 (tp30) REVERT: M 227 GLN cc_start: 0.7176 (pm20) cc_final: 0.6865 (pm20) REVERT: M 300 PHE cc_start: 0.8101 (m-80) cc_final: 0.7736 (m-80) REVERT: O 328 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8899 (tp) REVERT: R 145 LEU cc_start: 0.8263 (mm) cc_final: 0.7768 (tp) REVERT: R 170 LYS cc_start: 0.8178 (tmmt) cc_final: 0.7900 (tmmt) REVERT: U 358 MET cc_start: 0.6852 (ppp) cc_final: 0.4196 (tmt) REVERT: W 76 MET cc_start: 0.3850 (mmm) cc_final: 0.3410 (mmp) outliers start: 112 outliers final: 41 residues processed: 683 average time/residue: 0.8638 time to fit residues: 709.3600 Evaluate side-chains 663 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 607 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 45 GLN Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain Q residue 177 MET Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 48 MET Chi-restraints excluded: chain W residue 66 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 404 optimal weight: 7.9990 chunk 425 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 301 optimal weight: 0.9980 chunk 481 optimal weight: 0.0020 chunk 250 optimal weight: 5.9990 chunk 487 optimal weight: 10.0000 chunk 490 optimal weight: 10.0000 chunk 310 optimal weight: 1.9990 chunk 525 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 861 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 ASN A1251 ASN A1299 GLN A1310 HIS B 552 ASN B 649 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN H 76 ASN J 52 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 ASN M 263 GLN O 256 GLN Q 168 ASN R 144 GLN X 188 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.201758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.128668 restraints weight = 46523.034| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.75 r_work: 0.2948 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.147 45270 Z= 0.373 Angle : 0.698 26.340 61482 Z= 0.352 Chirality : 0.050 0.301 6849 Planarity : 0.006 0.087 7660 Dihedral : 12.445 59.938 6734 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.07 % Allowed : 12.75 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.11), residues: 5233 helix: 0.85 (0.11), residues: 1980 sheet: 0.34 (0.18), residues: 819 loop : -0.08 (0.13), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 47 TYR 0.026 0.002 TYR A 413 PHE 0.036 0.003 PHE A 592 TRP 0.022 0.003 TRP C 203 HIS 0.018 0.002 HIS M 18 Details of bonding type rmsd covalent geometry : bond 0.00881 (45231) covalent geometry : angle 0.67505 (61434) hydrogen bonds : bond 0.05421 ( 1201) hydrogen bonds : angle 4.06310 ( 3431) metal coordination : bond 0.02640 ( 39) metal coordination : angle 6.40664 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 614 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8540 (mmt90) cc_final: 0.8283 (mpt-90) REVERT: A 67 ARG cc_start: 0.7936 (mmm160) cc_final: 0.7123 (mmm160) REVERT: A 220 ARG cc_start: 0.8645 (tpt-90) cc_final: 0.7685 (tpm-80) REVERT: A 296 ASN cc_start: 0.7655 (m-40) cc_final: 0.7345 (m110) REVERT: A 423 ASN cc_start: 0.7703 (p0) cc_final: 0.7350 (p0) REVERT: A 425 ASP cc_start: 0.8116 (m-30) cc_final: 0.7691 (m-30) REVERT: A 439 HIS cc_start: 0.7486 (t70) cc_final: 0.7017 (m-70) REVERT: A 914 LYS cc_start: 0.8059 (tttp) cc_final: 0.7732 (ttpt) REVERT: A 1147 SER cc_start: 0.8408 (OUTLIER) cc_final: 0.8160 (p) REVERT: A 1155 LYS cc_start: 0.7714 (ttpt) cc_final: 0.7291 (tttm) REVERT: A 1162 GLU cc_start: 0.8359 (tt0) cc_final: 0.7869 (tt0) REVERT: A 1219 LYS cc_start: 0.8538 (tppt) cc_final: 0.8297 (tppt) REVERT: A 1288 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8695 (mp) REVERT: A 1306 LYS cc_start: 0.8357 (ttmm) cc_final: 0.7761 (tppt) REVERT: A 1416 ARG cc_start: 0.8790 (ptt90) cc_final: 0.8465 (ptt90) REVERT: A 1437 ASP cc_start: 0.8140 (m-30) cc_final: 0.7898 (m-30) REVERT: A 1472 ASP cc_start: 0.8646 (m-30) cc_final: 0.8364 (m-30) REVERT: B 24 GLU cc_start: 0.7882 (mp0) cc_final: 0.7557 (tm-30) REVERT: B 143 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8143 (pm20) REVERT: B 287 HIS cc_start: 0.8638 (m90) cc_final: 0.8363 (m90) REVERT: B 291 ASP cc_start: 0.8108 (t0) cc_final: 0.7781 (t0) REVERT: B 312 GLN cc_start: 0.8425 (mt0) cc_final: 0.8112 (mt0) REVERT: B 581 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: B 582 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8341 (tm130) REVERT: B 731 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8664 (mt0) REVERT: B 1081 ASP cc_start: 0.7021 (t0) cc_final: 0.6657 (t0) REVERT: B 1104 ARG cc_start: 0.9158 (ttt-90) cc_final: 0.8837 (ttp-170) REVERT: C 17 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: E 92 GLN cc_start: 0.8608 (tp40) cc_final: 0.8195 (tp-100) REVERT: E 101 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7848 (mtp180) REVERT: E 116 GLN cc_start: 0.8596 (tp40) cc_final: 0.8237 (tp40) REVERT: E 117 SER cc_start: 0.9306 (t) cc_final: 0.9019 (p) REVERT: E 131 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8566 (mm) REVERT: E 133 GLN cc_start: 0.8410 (tp-100) cc_final: 0.8086 (tp-100) REVERT: E 210 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6950 (tt0) REVERT: G 44 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.7150 (m-10) REVERT: G 104 MET cc_start: 0.7748 (ptm) cc_final: 0.6854 (ppp) REVERT: H 95 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8670 (ttpt) REVERT: H 103 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6864 (pm20) REVERT: H 111 ARG cc_start: 0.8239 (mmm-85) cc_final: 0.7934 (mtp-110) REVERT: H 123 MET cc_start: 0.9452 (ttp) cc_final: 0.9225 (ttp) REVERT: I 41 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7022 (m110) REVERT: I 56 ASN cc_start: 0.8955 (t0) cc_final: 0.8462 (t0) REVERT: I 82 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7985 (tp30) REVERT: I 109 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8143 (ptp90) REVERT: L 47 LYS cc_start: 0.8199 (ptmt) cc_final: 0.7952 (ptmm) REVERT: M 52 TRP cc_start: 0.7825 (p90) cc_final: 0.7403 (p90) REVERT: M 86 LYS cc_start: 0.7778 (mttt) cc_final: 0.7007 (mtpp) REVERT: M 227 GLN cc_start: 0.7263 (pm20) cc_final: 0.6951 (pm20) REVERT: M 300 PHE cc_start: 0.8125 (m-80) cc_final: 0.7681 (m-80) REVERT: O 167 ASN cc_start: 0.8387 (t0) cc_final: 0.7955 (m-40) REVERT: R 181 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8438 (tp-100) REVERT: U 358 MET cc_start: 0.6997 (ppp) cc_final: 0.4158 (tmt) REVERT: W 76 MET cc_start: 0.3973 (mmm) cc_final: 0.3548 (mmp) outliers start: 144 outliers final: 60 residues processed: 696 average time/residue: 0.8829 time to fit residues: 738.7755 Evaluate side-chains 663 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 588 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 892 CYS Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 101 ARG Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 109 ARG Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain W residue 48 MET Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 146 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 260 optimal weight: 0.6980 chunk 371 optimal weight: 0.5980 chunk 351 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 382 optimal weight: 0.4980 chunk 112 optimal weight: 4.9990 chunk 391 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 408 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 4 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1310 HIS B 552 ASN B 585 ASN B 842 HIS ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN H 76 ASN I 100 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.204939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.131229 restraints weight = 46511.900| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.75 r_work: 0.3027 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 45270 Z= 0.137 Angle : 0.546 26.600 61482 Z= 0.274 Chirality : 0.042 0.216 6849 Planarity : 0.004 0.084 7660 Dihedral : 12.317 59.859 6734 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.22 % Allowed : 14.43 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.12), residues: 5233 helix: 1.12 (0.12), residues: 1978 sheet: 0.37 (0.18), residues: 842 loop : -0.03 (0.13), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 51 TYR 0.016 0.001 TYR I 37 PHE 0.027 0.001 PHE G 107 TRP 0.020 0.001 TRP C 203 HIS 0.010 0.001 HIS M 18 Details of bonding type rmsd covalent geometry : bond 0.00311 (45231) covalent geometry : angle 0.52340 (61434) hydrogen bonds : bond 0.04011 ( 1201) hydrogen bonds : angle 3.77587 ( 3431) metal coordination : bond 0.01703 ( 39) metal coordination : angle 5.60435 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 625 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8526 (mmt90) cc_final: 0.8207 (mpt-90) REVERT: A 58 MET cc_start: 0.8682 (mmp) cc_final: 0.8459 (mmt) REVERT: A 67 ARG cc_start: 0.7967 (mmm160) cc_final: 0.7125 (mmm160) REVERT: A 220 ARG cc_start: 0.8597 (tpt-90) cc_final: 0.7638 (tpm-80) REVERT: A 296 ASN cc_start: 0.7810 (m-40) cc_final: 0.7550 (m110) REVERT: A 439 HIS cc_start: 0.7532 (t70) cc_final: 0.7064 (m-70) REVERT: A 715 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: A 852 VAL cc_start: 0.8427 (t) cc_final: 0.8213 (m) REVERT: A 914 LYS cc_start: 0.8063 (tttp) cc_final: 0.7743 (ttpt) REVERT: A 943 LEU cc_start: 0.8595 (mt) cc_final: 0.8385 (mt) REVERT: A 1035 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: A 1071 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8148 (tm-30) REVERT: A 1147 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7882 (p) REVERT: A 1150 ASP cc_start: 0.7098 (t70) cc_final: 0.6782 (p0) REVERT: A 1155 LYS cc_start: 0.7688 (ttpt) cc_final: 0.7236 (tttm) REVERT: A 1162 GLU cc_start: 0.8351 (tt0) cc_final: 0.7850 (tt0) REVERT: A 1228 MET cc_start: 0.8833 (mmm) cc_final: 0.8253 (mtt) REVERT: A 1288 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8597 (mp) REVERT: A 1306 LYS cc_start: 0.8402 (ttmm) cc_final: 0.7707 (tppt) REVERT: A 1308 TYR cc_start: 0.7979 (m-80) cc_final: 0.7737 (m-80) REVERT: A 1334 TRP cc_start: 0.9123 (m100) cc_final: 0.8905 (m100) REVERT: A 1416 ARG cc_start: 0.8798 (ptt90) cc_final: 0.8546 (ptt90) REVERT: A 1437 ASP cc_start: 0.8119 (m-30) cc_final: 0.7834 (m-30) REVERT: A 1472 ASP cc_start: 0.8648 (m-30) cc_final: 0.8376 (m-30) REVERT: B 24 GLU cc_start: 0.7800 (mp0) cc_final: 0.7506 (tm-30) REVERT: B 143 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8129 (pm20) REVERT: B 287 HIS cc_start: 0.8547 (m90) cc_final: 0.8235 (m90) REVERT: B 291 ASP cc_start: 0.8037 (t0) cc_final: 0.7720 (t0) REVERT: B 307 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: B 581 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: B 582 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8363 (tm130) REVERT: B 677 MET cc_start: 0.9177 (tpp) cc_final: 0.8847 (tpt) REVERT: B 731 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8649 (mt0) REVERT: B 1081 ASP cc_start: 0.6722 (t0) cc_final: 0.6461 (t0) REVERT: B 1104 ARG cc_start: 0.9134 (ttt-90) cc_final: 0.8820 (ttp-170) REVERT: C 17 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8029 (mt-10) REVERT: C 86 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7333 (ptt90) REVERT: C 154 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8159 (ptm160) REVERT: E 41 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.7763 (mmtt) REVERT: E 92 GLN cc_start: 0.8613 (tp40) cc_final: 0.8179 (tp-100) REVERT: E 116 GLN cc_start: 0.8544 (tp40) cc_final: 0.7914 (tp40) REVERT: E 117 SER cc_start: 0.9241 (t) cc_final: 0.8953 (p) REVERT: E 131 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8415 (mm) REVERT: E 133 GLN cc_start: 0.8404 (tp-100) cc_final: 0.8113 (tp-100) REVERT: E 210 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6874 (tt0) REVERT: F 59 LYS cc_start: 0.9366 (ptpt) cc_final: 0.9066 (ptmt) REVERT: G 2 PHE cc_start: 0.6656 (m-10) cc_final: 0.6208 (m-10) REVERT: G 44 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.7150 (m-10) REVERT: G 104 MET cc_start: 0.7761 (ptm) cc_final: 0.6919 (ppp) REVERT: H 111 ARG cc_start: 0.8227 (mmm-85) cc_final: 0.7922 (mtp-110) REVERT: H 123 MET cc_start: 0.9353 (ttp) cc_final: 0.9089 (ttp) REVERT: I 56 ASN cc_start: 0.8966 (t0) cc_final: 0.8435 (t0) REVERT: I 82 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7973 (tp30) REVERT: K 48 SER cc_start: 0.8926 (p) cc_final: 0.8716 (m) REVERT: L 37 ARG cc_start: 0.7249 (mmt180) cc_final: 0.6728 (ptp-110) REVERT: M 52 TRP cc_start: 0.7779 (p90) cc_final: 0.7338 (p90) REVERT: M 86 LYS cc_start: 0.7802 (mttt) cc_final: 0.7040 (mtpp) REVERT: M 190 GLU cc_start: 0.7997 (tp30) cc_final: 0.7651 (tp30) REVERT: M 227 GLN cc_start: 0.7173 (pm20) cc_final: 0.6893 (pm20) REVERT: M 300 PHE cc_start: 0.8078 (m-80) cc_final: 0.7699 (m-80) REVERT: R 145 LEU cc_start: 0.8272 (mm) cc_final: 0.7248 (tp) REVERT: U 358 MET cc_start: 0.7036 (ppp) cc_final: 0.4080 (tmt) REVERT: W 76 MET cc_start: 0.3824 (mmm) cc_final: 0.3432 (mmp) outliers start: 104 outliers final: 36 residues processed: 678 average time/residue: 0.8778 time to fit residues: 713.8431 Evaluate side-chains 650 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 597 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1035 GLU Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1339 ASP Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 48 MET Chi-restraints excluded: chain W residue 66 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 24 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 55 optimal weight: 0.0470 chunk 46 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 333 optimal weight: 50.0000 chunk 47 optimal weight: 0.0870 chunk 259 optimal weight: 1.9990 chunk 340 optimal weight: 0.9990 chunk 397 optimal weight: 0.7980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 ASN ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1445 HIS B 111 ASN B 420 GLN B 500 GLN B 585 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN H 76 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.205211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.132481 restraints weight = 46626.727| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.65 r_work: 0.3056 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 45270 Z= 0.123 Angle : 0.540 24.103 61482 Z= 0.269 Chirality : 0.041 0.217 6849 Planarity : 0.004 0.069 7660 Dihedral : 12.266 59.892 6734 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.26 % Allowed : 15.24 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.12), residues: 5233 helix: 1.24 (0.12), residues: 1978 sheet: 0.34 (0.18), residues: 849 loop : -0.00 (0.13), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG R 51 TYR 0.021 0.001 TYR B 160 PHE 0.027 0.001 PHE G 107 TRP 0.019 0.001 TRP B 27 HIS 0.008 0.001 HIS M 18 Details of bonding type rmsd covalent geometry : bond 0.00279 (45231) covalent geometry : angle 0.51962 (61434) hydrogen bonds : bond 0.03820 ( 1201) hydrogen bonds : angle 3.71247 ( 3431) metal coordination : bond 0.01528 ( 39) metal coordination : angle 5.23121 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 624 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8494 (mmt90) cc_final: 0.8172 (mpt-90) REVERT: A 58 MET cc_start: 0.8648 (mmp) cc_final: 0.8378 (mmt) REVERT: A 67 ARG cc_start: 0.7931 (mmm160) cc_final: 0.7274 (mtp180) REVERT: A 220 ARG cc_start: 0.8489 (tpt-90) cc_final: 0.7492 (tpm-80) REVERT: A 226 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7934 (mtpt) REVERT: A 296 ASN cc_start: 0.7769 (m-40) cc_final: 0.7435 (m110) REVERT: A 439 HIS cc_start: 0.7403 (t70) cc_final: 0.6954 (m-70) REVERT: A 914 LYS cc_start: 0.8018 (tttp) cc_final: 0.7689 (ttpt) REVERT: A 943 LEU cc_start: 0.8520 (mt) cc_final: 0.8299 (mt) REVERT: A 1071 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: A 1155 LYS cc_start: 0.7560 (ttpt) cc_final: 0.7013 (tttm) REVERT: A 1162 GLU cc_start: 0.8400 (tt0) cc_final: 0.7942 (tt0) REVERT: A 1219 LYS cc_start: 0.8296 (tppt) cc_final: 0.8045 (tppt) REVERT: A 1288 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8604 (mp) REVERT: A 1306 LYS cc_start: 0.8270 (ttmm) cc_final: 0.7618 (tppt) REVERT: A 1308 TYR cc_start: 0.7968 (m-80) cc_final: 0.7685 (m-80) REVERT: A 1416 ARG cc_start: 0.8833 (ptt90) cc_final: 0.8543 (ptt90) REVERT: A 1437 ASP cc_start: 0.8144 (m-30) cc_final: 0.7851 (m-30) REVERT: A 1472 ASP cc_start: 0.8600 (m-30) cc_final: 0.8322 (m-30) REVERT: B 24 GLU cc_start: 0.7729 (mp0) cc_final: 0.7448 (tm-30) REVERT: B 143 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8082 (pm20) REVERT: B 287 HIS cc_start: 0.8523 (m90) cc_final: 0.8241 (m90) REVERT: B 291 ASP cc_start: 0.8063 (t0) cc_final: 0.7728 (t0) REVERT: B 298 MET cc_start: 0.8486 (mtp) cc_final: 0.8165 (mtp) REVERT: B 581 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: B 582 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8374 (tm130) REVERT: B 677 MET cc_start: 0.9192 (tpp) cc_final: 0.8833 (tpt) REVERT: B 731 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8647 (mt0) REVERT: B 1104 ARG cc_start: 0.9140 (ttt-90) cc_final: 0.8822 (ttp-170) REVERT: C 17 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8163 (mt-10) REVERT: C 86 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7153 (ptt90) REVERT: C 154 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8077 (ptm160) REVERT: E 41 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7749 (mmtt) REVERT: E 92 GLN cc_start: 0.8618 (tp40) cc_final: 0.8171 (tp-100) REVERT: E 116 GLN cc_start: 0.8520 (tp40) cc_final: 0.7934 (tp40) REVERT: E 117 SER cc_start: 0.9219 (t) cc_final: 0.8898 (p) REVERT: E 131 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8310 (mm) REVERT: E 133 GLN cc_start: 0.8375 (tp-100) cc_final: 0.8084 (tp-100) REVERT: E 210 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6793 (tt0) REVERT: F 59 LYS cc_start: 0.9342 (ptpt) cc_final: 0.9018 (ptmt) REVERT: G 25 THR cc_start: 0.9458 (m) cc_final: 0.9217 (m) REVERT: G 44 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.7117 (m-10) REVERT: H 72 ASP cc_start: 0.7047 (t0) cc_final: 0.6678 (t0) REVERT: H 74 GLU cc_start: 0.7971 (pm20) cc_final: 0.7703 (tt0) REVERT: H 98 ARG cc_start: 0.8973 (ttm-80) cc_final: 0.8706 (ttt90) REVERT: H 111 ARG cc_start: 0.8200 (mmm-85) cc_final: 0.7920 (mtp-110) REVERT: H 123 MET cc_start: 0.9340 (ttp) cc_final: 0.9044 (ttp) REVERT: I 56 ASN cc_start: 0.8956 (t0) cc_final: 0.8378 (t0) REVERT: J 41 LYS cc_start: 0.8909 (mttp) cc_final: 0.8673 (mmpt) REVERT: M 52 TRP cc_start: 0.7728 (p90) cc_final: 0.7266 (p90) REVERT: M 86 LYS cc_start: 0.7757 (mttt) cc_final: 0.6976 (mtpp) REVERT: M 190 GLU cc_start: 0.8003 (tp30) cc_final: 0.7650 (tp30) REVERT: M 227 GLN cc_start: 0.7206 (pm20) cc_final: 0.6865 (pm20) REVERT: M 300 PHE cc_start: 0.8033 (m-80) cc_final: 0.7748 (m-80) REVERT: O 166 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7900 (mp10) REVERT: O 167 ASN cc_start: 0.8149 (t0) cc_final: 0.7745 (m-40) REVERT: O 229 GLN cc_start: 0.8391 (mm-40) cc_final: 0.7722 (tp-100) REVERT: R 145 LEU cc_start: 0.8301 (mm) cc_final: 0.7769 (tp) REVERT: U 358 MET cc_start: 0.6862 (ppp) cc_final: 0.4041 (tmt) REVERT: W 76 MET cc_start: 0.3859 (mmm) cc_final: 0.3568 (mmp) outliers start: 106 outliers final: 45 residues processed: 685 average time/residue: 0.7996 time to fit residues: 658.1577 Evaluate side-chains 648 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 591 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 303 ASP Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain W residue 48 MET Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 115 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 371 optimal weight: 0.5980 chunk 517 optimal weight: 50.0000 chunk 50 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 chunk 404 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 283 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN R 144 GLN W 101 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.204222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.130996 restraints weight = 46461.049| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.75 r_work: 0.3005 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 45270 Z= 0.190 Angle : 0.580 23.563 61482 Z= 0.289 Chirality : 0.043 0.217 6849 Planarity : 0.004 0.069 7660 Dihedral : 12.338 59.858 6734 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.16 % Allowed : 15.78 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.12), residues: 5233 helix: 1.16 (0.12), residues: 1978 sheet: 0.32 (0.18), residues: 839 loop : -0.04 (0.13), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 51 TYR 0.025 0.002 TYR B 160 PHE 0.024 0.002 PHE A 592 TRP 0.018 0.002 TRP B 27 HIS 0.011 0.001 HIS M 18 Details of bonding type rmsd covalent geometry : bond 0.00442 (45231) covalent geometry : angle 0.56021 (61434) hydrogen bonds : bond 0.04179 ( 1201) hydrogen bonds : angle 3.77408 ( 3431) metal coordination : bond 0.01925 ( 39) metal coordination : angle 5.37592 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 605 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8492 (mmt90) cc_final: 0.8160 (mpt-90) REVERT: A 67 ARG cc_start: 0.7937 (mmm160) cc_final: 0.7301 (mtp180) REVERT: A 220 ARG cc_start: 0.8575 (tpt-90) cc_final: 0.7615 (tpm-80) REVERT: A 296 ASN cc_start: 0.7735 (m-40) cc_final: 0.7403 (m110) REVERT: A 329 MET cc_start: 0.8632 (mmm) cc_final: 0.8292 (mmm) REVERT: A 425 ASP cc_start: 0.8149 (m-30) cc_final: 0.7815 (m-30) REVERT: A 439 HIS cc_start: 0.7450 (t70) cc_final: 0.7002 (m-70) REVERT: A 914 LYS cc_start: 0.8029 (tttp) cc_final: 0.7577 (tttt) REVERT: A 943 LEU cc_start: 0.8530 (mt) cc_final: 0.8301 (mt) REVERT: A 1052 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7022 (tpp-160) REVERT: A 1071 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: A 1155 LYS cc_start: 0.7636 (ttpt) cc_final: 0.7236 (tttm) REVERT: A 1162 GLU cc_start: 0.8402 (tt0) cc_final: 0.7882 (tt0) REVERT: A 1219 LYS cc_start: 0.8474 (tppt) cc_final: 0.8188 (tppt) REVERT: A 1288 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8575 (mp) REVERT: A 1306 LYS cc_start: 0.8261 (ttmm) cc_final: 0.7608 (tppt) REVERT: A 1308 TYR cc_start: 0.8011 (m-80) cc_final: 0.7739 (m-80) REVERT: A 1416 ARG cc_start: 0.8853 (ptt90) cc_final: 0.8575 (ptt90) REVERT: A 1422 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7347 (mm110) REVERT: A 1437 ASP cc_start: 0.8131 (m-30) cc_final: 0.7838 (m-30) REVERT: A 1472 ASP cc_start: 0.8603 (m-30) cc_final: 0.8299 (m-30) REVERT: B 24 GLU cc_start: 0.7724 (mp0) cc_final: 0.7395 (tm-30) REVERT: B 143 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8143 (pm20) REVERT: B 287 HIS cc_start: 0.8584 (m90) cc_final: 0.8264 (m90) REVERT: B 291 ASP cc_start: 0.8017 (t0) cc_final: 0.7700 (t0) REVERT: B 298 MET cc_start: 0.8502 (mtp) cc_final: 0.8195 (mtp) REVERT: B 581 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: B 582 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8338 (tm130) REVERT: B 677 MET cc_start: 0.9146 (tpp) cc_final: 0.8775 (tpt) REVERT: B 731 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8672 (mt0) REVERT: B 1104 ARG cc_start: 0.9163 (ttt-90) cc_final: 0.8835 (ttp-170) REVERT: C 17 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: C 41 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7972 (mp0) REVERT: C 86 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7295 (ptt90) REVERT: C 154 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8195 (ptm160) REVERT: E 41 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7759 (mmtt) REVERT: E 92 GLN cc_start: 0.8665 (tp40) cc_final: 0.8218 (tp-100) REVERT: E 101 ARG cc_start: 0.8513 (mtp180) cc_final: 0.7975 (mtp180) REVERT: E 116 GLN cc_start: 0.8536 (tp40) cc_final: 0.7971 (tp40) REVERT: E 117 SER cc_start: 0.9178 (t) cc_final: 0.8893 (p) REVERT: E 131 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8417 (mm) REVERT: E 133 GLN cc_start: 0.8406 (tp-100) cc_final: 0.8111 (tp-100) REVERT: E 210 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6874 (tt0) REVERT: F 59 LYS cc_start: 0.9376 (ptpt) cc_final: 0.9061 (ptmt) REVERT: G 25 THR cc_start: 0.9459 (m) cc_final: 0.9229 (m) REVERT: G 44 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.7118 (m-10) REVERT: H 72 ASP cc_start: 0.7209 (t0) cc_final: 0.6807 (t0) REVERT: H 74 GLU cc_start: 0.8011 (pm20) cc_final: 0.7664 (tt0) REVERT: H 111 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.7900 (mtp-110) REVERT: H 123 MET cc_start: 0.9396 (ttp) cc_final: 0.9128 (ttp) REVERT: I 41 ASN cc_start: 0.7544 (m-40) cc_final: 0.7188 (m-40) REVERT: I 56 ASN cc_start: 0.9092 (t0) cc_final: 0.8812 (t0) REVERT: L 37 ARG cc_start: 0.7271 (mmt180) cc_final: 0.6696 (ptp-110) REVERT: M 52 TRP cc_start: 0.7773 (p90) cc_final: 0.7313 (p90) REVERT: M 86 LYS cc_start: 0.7750 (mttt) cc_final: 0.6976 (mtpp) REVERT: M 190 GLU cc_start: 0.8086 (tp30) cc_final: 0.7632 (tp30) REVERT: M 227 GLN cc_start: 0.7195 (pm20) cc_final: 0.6905 (pm20) REVERT: M 300 PHE cc_start: 0.8062 (m-80) cc_final: 0.7820 (m-80) REVERT: O 229 GLN cc_start: 0.8438 (mm-40) cc_final: 0.7833 (tp-100) REVERT: R 145 LEU cc_start: 0.8360 (mm) cc_final: 0.7799 (mt) REVERT: U 358 MET cc_start: 0.6907 (ppp) cc_final: 0.6363 (ppp) outliers start: 101 outliers final: 51 residues processed: 666 average time/residue: 0.6238 time to fit residues: 501.9798 Evaluate side-chains 661 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 595 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1052 ARG Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1280 ASP Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1327 GLU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain W residue 48 MET Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 115 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 412 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 265 optimal weight: 0.3980 chunk 403 optimal weight: 8.9990 chunk 186 optimal weight: 1.9990 chunk 321 optimal weight: 0.8980 chunk 444 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 335 optimal weight: 40.0000 chunk 297 optimal weight: 0.8980 chunk 141 optimal weight: 0.0050 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN H 76 ASN K 69 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN R 144 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.206406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.125232 restraints weight = 47015.460| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.02 r_work: 0.3024 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 45270 Z= 0.141 Angle : 0.552 22.932 61482 Z= 0.274 Chirality : 0.042 0.208 6849 Planarity : 0.004 0.068 7660 Dihedral : 12.296 59.972 6734 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.92 % Allowed : 16.18 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.12), residues: 5233 helix: 1.23 (0.12), residues: 1982 sheet: 0.26 (0.18), residues: 835 loop : -0.04 (0.13), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG R 51 TYR 0.019 0.001 TYR B 160 PHE 0.023 0.001 PHE G 107 TRP 0.019 0.001 TRP A 479 HIS 0.010 0.001 HIS M 18 Details of bonding type rmsd covalent geometry : bond 0.00322 (45231) covalent geometry : angle 0.53276 (61434) hydrogen bonds : bond 0.03830 ( 1201) hydrogen bonds : angle 3.70937 ( 3431) metal coordination : bond 0.01721 ( 39) metal coordination : angle 5.13520 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 612 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8482 (mmt90) cc_final: 0.8129 (mpt-90) REVERT: A 67 ARG cc_start: 0.7997 (mmm160) cc_final: 0.7275 (mtp180) REVERT: A 104 MET cc_start: 0.8427 (mtp) cc_final: 0.8149 (mtp) REVERT: A 220 ARG cc_start: 0.8429 (tpt-90) cc_final: 0.7275 (tpm-80) REVERT: A 296 ASN cc_start: 0.7646 (m-40) cc_final: 0.7359 (m110) REVERT: A 329 MET cc_start: 0.8543 (mmm) cc_final: 0.8231 (mmm) REVERT: A 425 ASP cc_start: 0.8051 (m-30) cc_final: 0.7673 (m-30) REVERT: A 439 HIS cc_start: 0.7383 (t70) cc_final: 0.6903 (m-70) REVERT: A 715 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: A 914 LYS cc_start: 0.7846 (tttp) cc_final: 0.7343 (tttt) REVERT: A 943 LEU cc_start: 0.8369 (mt) cc_final: 0.8134 (mt) REVERT: A 1052 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.7108 (tpp-160) REVERT: A 1071 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: A 1155 LYS cc_start: 0.7407 (ttpt) cc_final: 0.7031 (tttm) REVERT: A 1162 GLU cc_start: 0.8515 (tt0) cc_final: 0.8011 (tt0) REVERT: A 1219 LYS cc_start: 0.8493 (tppt) cc_final: 0.8224 (tppt) REVERT: A 1288 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8390 (mp) REVERT: A 1306 LYS cc_start: 0.8238 (ttmm) cc_final: 0.7520 (tppt) REVERT: A 1308 TYR cc_start: 0.7979 (m-80) cc_final: 0.7645 (m-80) REVERT: A 1416 ARG cc_start: 0.8744 (ptt90) cc_final: 0.8449 (ptt90) REVERT: A 1437 ASP cc_start: 0.8256 (m-30) cc_final: 0.7919 (m-30) REVERT: A 1472 ASP cc_start: 0.8827 (m-30) cc_final: 0.8475 (m-30) REVERT: B 24 GLU cc_start: 0.7688 (mp0) cc_final: 0.7196 (tm-30) REVERT: B 143 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8203 (pm20) REVERT: B 287 HIS cc_start: 0.8578 (m90) cc_final: 0.8302 (m90) REVERT: B 291 ASP cc_start: 0.8090 (t0) cc_final: 0.7711 (t0) REVERT: B 581 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: B 582 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8323 (tm130) REVERT: B 677 MET cc_start: 0.9104 (tpp) cc_final: 0.8710 (tpt) REVERT: B 731 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8771 (mt0) REVERT: B 1104 ARG cc_start: 0.9210 (ttt-90) cc_final: 0.8889 (ttp-170) REVERT: C 17 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: C 86 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7095 (ptt90) REVERT: C 154 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8083 (ptm160) REVERT: E 41 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7712 (mmtt) REVERT: E 92 GLN cc_start: 0.8810 (tp40) cc_final: 0.8325 (tp-100) REVERT: E 101 ARG cc_start: 0.8558 (mtp180) cc_final: 0.7990 (mtp180) REVERT: E 116 GLN cc_start: 0.8550 (tp40) cc_final: 0.7933 (tp40) REVERT: E 117 SER cc_start: 0.9087 (t) cc_final: 0.8414 (p) REVERT: E 131 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8247 (mm) REVERT: E 133 GLN cc_start: 0.8398 (tp-100) cc_final: 0.8018 (tp-100) REVERT: E 210 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6909 (tt0) REVERT: F 59 LYS cc_start: 0.9380 (ptpt) cc_final: 0.9064 (ptmt) REVERT: G 25 THR cc_start: 0.9405 (m) cc_final: 0.9161 (m) REVERT: G 44 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7464 (m-10) REVERT: H 72 ASP cc_start: 0.7430 (t0) cc_final: 0.6999 (t0) REVERT: H 74 GLU cc_start: 0.8034 (pm20) cc_final: 0.7604 (tt0) REVERT: H 98 ARG cc_start: 0.8962 (ttm-80) cc_final: 0.8637 (ttt90) REVERT: H 111 ARG cc_start: 0.8112 (mmm-85) cc_final: 0.7859 (mtp-110) REVERT: H 123 MET cc_start: 0.9415 (ttp) cc_final: 0.9123 (ttp) REVERT: I 41 ASN cc_start: 0.7630 (m-40) cc_final: 0.7257 (m-40) REVERT: I 56 ASN cc_start: 0.9045 (t0) cc_final: 0.8674 (t0) REVERT: J 41 LYS cc_start: 0.8957 (mttp) cc_final: 0.8558 (mmpt) REVERT: K 48 SER cc_start: 0.8978 (p) cc_final: 0.8708 (m) REVERT: L 37 ARG cc_start: 0.7339 (mmt180) cc_final: 0.6633 (ptp-110) REVERT: M 36 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: M 52 TRP cc_start: 0.7414 (p90) cc_final: 0.6900 (p90) REVERT: M 86 LYS cc_start: 0.7708 (mttt) cc_final: 0.6854 (mtpp) REVERT: M 124 MET cc_start: 0.8981 (mtm) cc_final: 0.8744 (mtp) REVERT: M 190 GLU cc_start: 0.7995 (tp30) cc_final: 0.7526 (tp30) REVERT: M 227 GLN cc_start: 0.7115 (pm20) cc_final: 0.6769 (pm20) REVERT: M 300 PHE cc_start: 0.7954 (m-80) cc_final: 0.7744 (m-80) REVERT: O 166 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7767 (mp10) REVERT: O 229 GLN cc_start: 0.8495 (mm-40) cc_final: 0.7910 (tp-100) REVERT: R 122 GLU cc_start: 0.3825 (mm-30) cc_final: 0.2926 (mm-30) REVERT: R 145 LEU cc_start: 0.8332 (mm) cc_final: 0.7461 (tp) REVERT: R 181 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8432 (tp-100) REVERT: U 358 MET cc_start: 0.7063 (ppp) cc_final: 0.6396 (ppp) outliers start: 90 outliers final: 48 residues processed: 667 average time/residue: 0.5373 time to fit residues: 435.3995 Evaluate side-chains 660 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 597 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1052 ARG Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1327 GLU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 115 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 154 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 406 optimal weight: 5.9990 chunk 476 optimal weight: 0.0370 chunk 266 optimal weight: 1.9990 chunk 395 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 428 optimal weight: 0.9990 chunk 380 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 ASN ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 GLN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN H 76 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.207273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.123784 restraints weight = 46513.015| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.09 r_work: 0.3066 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 45270 Z= 0.141 Angle : 0.562 22.641 61482 Z= 0.277 Chirality : 0.042 0.264 6849 Planarity : 0.004 0.067 7660 Dihedral : 12.290 59.670 6734 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.81 % Allowed : 16.35 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.12), residues: 5233 helix: 1.24 (0.12), residues: 1980 sheet: 0.24 (0.18), residues: 827 loop : -0.04 (0.13), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG R 51 TYR 0.024 0.001 TYR B 648 PHE 0.020 0.001 PHE A 397 TRP 0.019 0.001 TRP B 27 HIS 0.010 0.001 HIS M 18 Details of bonding type rmsd covalent geometry : bond 0.00325 (45231) covalent geometry : angle 0.54418 (61434) hydrogen bonds : bond 0.03791 ( 1201) hydrogen bonds : angle 3.67920 ( 3431) metal coordination : bond 0.01727 ( 39) metal coordination : angle 5.10645 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 606 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8414 (mmt90) cc_final: 0.8047 (mpt-90) REVERT: A 58 MET cc_start: 0.8609 (mmp) cc_final: 0.8309 (mmt) REVERT: A 67 ARG cc_start: 0.7979 (mmm160) cc_final: 0.7250 (mtp180) REVERT: A 104 MET cc_start: 0.8326 (mtp) cc_final: 0.7984 (mtp) REVERT: A 220 ARG cc_start: 0.8345 (tpt-90) cc_final: 0.7242 (tpm-80) REVERT: A 296 ASN cc_start: 0.7578 (m-40) cc_final: 0.7273 (m110) REVERT: A 329 MET cc_start: 0.8423 (mmm) cc_final: 0.8080 (mmm) REVERT: A 425 ASP cc_start: 0.7931 (m-30) cc_final: 0.7523 (m-30) REVERT: A 430 ARG cc_start: 0.8625 (ptt-90) cc_final: 0.8106 (ptt-90) REVERT: A 439 HIS cc_start: 0.7310 (t70) cc_final: 0.6830 (m-70) REVERT: A 914 LYS cc_start: 0.7740 (tttp) cc_final: 0.7223 (tttt) REVERT: A 943 LEU cc_start: 0.8282 (mt) cc_final: 0.8051 (mt) REVERT: A 1052 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.6992 (tpp-160) REVERT: A 1071 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: A 1155 LYS cc_start: 0.7321 (ttpt) cc_final: 0.6856 (tttm) REVERT: A 1162 GLU cc_start: 0.8471 (tt0) cc_final: 0.7923 (tt0) REVERT: A 1219 LYS cc_start: 0.8545 (tppt) cc_final: 0.8270 (tppt) REVERT: A 1288 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8214 (mp) REVERT: A 1306 LYS cc_start: 0.8146 (ttmm) cc_final: 0.7410 (tppt) REVERT: A 1308 TYR cc_start: 0.7916 (m-80) cc_final: 0.7561 (m-80) REVERT: A 1422 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7023 (mm110) REVERT: A 1437 ASP cc_start: 0.8120 (m-30) cc_final: 0.7769 (m-30) REVERT: A 1472 ASP cc_start: 0.8764 (m-30) cc_final: 0.8381 (m-30) REVERT: B 24 GLU cc_start: 0.7513 (mp0) cc_final: 0.7038 (tm-30) REVERT: B 143 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8160 (pm20) REVERT: B 287 HIS cc_start: 0.8519 (m90) cc_final: 0.8265 (m90) REVERT: B 291 ASP cc_start: 0.8074 (t0) cc_final: 0.7680 (t0) REVERT: B 298 MET cc_start: 0.8491 (mtp) cc_final: 0.8133 (mtp) REVERT: B 581 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: B 582 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8164 (tm130) REVERT: B 677 MET cc_start: 0.9030 (tpp) cc_final: 0.8647 (tpt) REVERT: B 731 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8747 (mt0) REVERT: B 1104 ARG cc_start: 0.9155 (ttt-90) cc_final: 0.8827 (ttp-170) REVERT: C 17 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7834 (mt-10) REVERT: C 86 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7003 (ptt90) REVERT: C 154 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7967 (ptm160) REVERT: E 41 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7682 (mmtt) REVERT: E 92 GLN cc_start: 0.8814 (tp40) cc_final: 0.8311 (tp-100) REVERT: E 101 ARG cc_start: 0.8557 (mtp180) cc_final: 0.8011 (mtp180) REVERT: E 131 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8103 (mm) REVERT: E 133 GLN cc_start: 0.8340 (tp-100) cc_final: 0.7935 (tp-100) REVERT: E 210 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6796 (tt0) REVERT: F 59 LYS cc_start: 0.9327 (ptpt) cc_final: 0.8992 (ptmt) REVERT: G 25 THR cc_start: 0.9372 (m) cc_final: 0.9127 (m) REVERT: G 44 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7493 (m-10) REVERT: G 46 ILE cc_start: 0.8557 (mp) cc_final: 0.7981 (mp) REVERT: H 74 GLU cc_start: 0.7974 (pm20) cc_final: 0.7554 (tt0) REVERT: H 98 ARG cc_start: 0.8872 (ttm-80) cc_final: 0.8561 (ttt90) REVERT: H 111 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7800 (mtp-110) REVERT: H 123 MET cc_start: 0.9410 (ttp) cc_final: 0.9118 (ttp) REVERT: I 51 SER cc_start: 0.8003 (p) cc_final: 0.7744 (t) REVERT: I 56 ASN cc_start: 0.8999 (t0) cc_final: 0.8649 (t0) REVERT: K 48 SER cc_start: 0.8864 (p) cc_final: 0.8584 (m) REVERT: L 37 ARG cc_start: 0.7290 (mmt180) cc_final: 0.6569 (ptp-110) REVERT: M 36 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: M 52 TRP cc_start: 0.7424 (p90) cc_final: 0.6995 (p90) REVERT: M 86 LYS cc_start: 0.7650 (mttt) cc_final: 0.6777 (mtpp) REVERT: M 124 MET cc_start: 0.8906 (mtm) cc_final: 0.8661 (mtp) REVERT: M 190 GLU cc_start: 0.7861 (tp30) cc_final: 0.7394 (tp30) REVERT: M 227 GLN cc_start: 0.7085 (pm20) cc_final: 0.6739 (pm20) REVERT: M 300 PHE cc_start: 0.7923 (m-80) cc_final: 0.7719 (m-80) REVERT: O 229 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8006 (tp-100) REVERT: R 122 GLU cc_start: 0.3460 (mm-30) cc_final: 0.2763 (mm-30) REVERT: R 145 LEU cc_start: 0.7994 (mm) cc_final: 0.7145 (tp) REVERT: R 181 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8489 (tp-100) REVERT: U 358 MET cc_start: 0.7063 (ppp) cc_final: 0.6388 (ppp) REVERT: W 48 MET cc_start: 0.5200 (mtt) cc_final: 0.4837 (mpt) REVERT: W 76 MET cc_start: 0.2481 (mmm) cc_final: 0.2227 (mmp) outliers start: 85 outliers final: 53 residues processed: 661 average time/residue: 0.5229 time to fit residues: 419.5828 Evaluate side-chains 665 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 597 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1052 ARG Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1280 ASP Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1327 GLU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 303 ASP Chi-restraints excluded: chain O residue 191 GLU Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 115 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 40 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 155 optimal weight: 0.4980 chunk 163 optimal weight: 0.0370 chunk 5 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 154 optimal weight: 0.3980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 ASN A1310 HIS B 312 GLN B 654 GLN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN H 76 ASN I 22 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN R 144 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.207610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123650 restraints weight = 46719.285| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.63 r_work: 0.3033 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 45270 Z= 0.128 Angle : 0.560 22.048 61482 Z= 0.276 Chirality : 0.042 0.228 6849 Planarity : 0.004 0.063 7660 Dihedral : 12.279 59.905 6734 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.47 % Allowed : 16.76 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.12), residues: 5233 helix: 1.29 (0.12), residues: 1976 sheet: 0.25 (0.18), residues: 819 loop : -0.06 (0.13), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 241 TYR 0.026 0.001 TYR B 648 PHE 0.024 0.001 PHE G 107 TRP 0.022 0.001 TRP A1334 HIS 0.009 0.001 HIS M 18 Details of bonding type rmsd covalent geometry : bond 0.00293 (45231) covalent geometry : angle 0.54264 (61434) hydrogen bonds : bond 0.03663 ( 1201) hydrogen bonds : angle 3.67305 ( 3431) metal coordination : bond 0.01429 ( 39) metal coordination : angle 4.99412 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 615 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8493 (mmt90) cc_final: 0.8155 (mpt-90) REVERT: A 58 MET cc_start: 0.8709 (mmp) cc_final: 0.8436 (mmt) REVERT: A 67 ARG cc_start: 0.7997 (mmm160) cc_final: 0.7294 (mtp180) REVERT: A 104 MET cc_start: 0.8505 (mtp) cc_final: 0.8185 (mtp) REVERT: A 220 ARG cc_start: 0.8433 (tpt-90) cc_final: 0.7298 (tpm-80) REVERT: A 295 GLN cc_start: 0.8003 (mt0) cc_final: 0.7786 (mm-40) REVERT: A 296 ASN cc_start: 0.7726 (m-40) cc_final: 0.7425 (m110) REVERT: A 329 MET cc_start: 0.8574 (mmm) cc_final: 0.8264 (mmm) REVERT: A 425 ASP cc_start: 0.8096 (m-30) cc_final: 0.7720 (m-30) REVERT: A 430 ARG cc_start: 0.8679 (ptt-90) cc_final: 0.8162 (ptt-90) REVERT: A 439 HIS cc_start: 0.7394 (t70) cc_final: 0.6920 (m-70) REVERT: A 762 GLU cc_start: 0.8195 (pm20) cc_final: 0.7962 (pp20) REVERT: A 914 LYS cc_start: 0.7849 (tttp) cc_final: 0.7344 (tttt) REVERT: A 943 LEU cc_start: 0.8346 (mt) cc_final: 0.8128 (mt) REVERT: A 1052 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.7154 (tpp-160) REVERT: A 1071 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8085 (tm-30) REVERT: A 1155 LYS cc_start: 0.7372 (ttpt) cc_final: 0.6885 (tttm) REVERT: A 1162 GLU cc_start: 0.8533 (tt0) cc_final: 0.8052 (tt0) REVERT: A 1219 LYS cc_start: 0.8567 (tppt) cc_final: 0.8319 (tppt) REVERT: A 1288 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8362 (mp) REVERT: A 1306 LYS cc_start: 0.8277 (ttmm) cc_final: 0.7568 (tppt) REVERT: A 1308 TYR cc_start: 0.8077 (m-80) cc_final: 0.7655 (m-80) REVERT: A 1332 GLN cc_start: 0.8276 (tp-100) cc_final: 0.7935 (tp-100) REVERT: A 1351 ASP cc_start: 0.8782 (m-30) cc_final: 0.8332 (t0) REVERT: A 1422 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7049 (mm110) REVERT: A 1437 ASP cc_start: 0.8341 (m-30) cc_final: 0.7999 (m-30) REVERT: A 1472 ASP cc_start: 0.8818 (m-30) cc_final: 0.8467 (m-30) REVERT: B 24 GLU cc_start: 0.7697 (mp0) cc_final: 0.7213 (tm-30) REVERT: B 143 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8207 (pm20) REVERT: B 287 HIS cc_start: 0.8606 (m90) cc_final: 0.8396 (m90) REVERT: B 291 ASP cc_start: 0.8108 (t0) cc_final: 0.7723 (t0) REVERT: B 582 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8301 (tm130) REVERT: B 677 MET cc_start: 0.9121 (tpp) cc_final: 0.8750 (tpt) REVERT: B 731 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8786 (mt0) REVERT: B 1104 ARG cc_start: 0.9218 (ttt-90) cc_final: 0.8895 (ttp-170) REVERT: C 17 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: C 154 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.8048 (ptm160) REVERT: E 18 MET cc_start: 0.8966 (mmp) cc_final: 0.8734 (mpp) REVERT: E 41 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7684 (mmtt) REVERT: E 92 GLN cc_start: 0.8835 (tp40) cc_final: 0.8326 (tp-100) REVERT: E 131 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8256 (mm) REVERT: E 133 GLN cc_start: 0.8396 (tp-100) cc_final: 0.8014 (tp-100) REVERT: E 210 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.6922 (tt0) REVERT: F 59 LYS cc_start: 0.9377 (ptpt) cc_final: 0.9054 (ptmt) REVERT: G 2 PHE cc_start: 0.6380 (m-10) cc_final: 0.6134 (m-10) REVERT: G 44 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7483 (m-10) REVERT: G 46 ILE cc_start: 0.8510 (mp) cc_final: 0.7972 (mp) REVERT: G 77 PHE cc_start: 0.6201 (t80) cc_final: 0.5858 (OUTLIER) REVERT: H 74 GLU cc_start: 0.7993 (pm20) cc_final: 0.7654 (tt0) REVERT: H 98 ARG cc_start: 0.8920 (ttm-80) cc_final: 0.8494 (ttt90) REVERT: H 111 ARG cc_start: 0.8135 (mmm-85) cc_final: 0.7890 (mtp-110) REVERT: H 123 MET cc_start: 0.9423 (ttp) cc_final: 0.9158 (ttp) REVERT: I 51 SER cc_start: 0.8088 (p) cc_final: 0.7844 (t) REVERT: I 56 ASN cc_start: 0.9033 (t0) cc_final: 0.8705 (t0) REVERT: K 48 SER cc_start: 0.8868 (p) cc_final: 0.8624 (m) REVERT: L 37 ARG cc_start: 0.7325 (mmt180) cc_final: 0.6632 (ptp-110) REVERT: M 36 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: M 52 TRP cc_start: 0.7486 (p90) cc_final: 0.7049 (p90) REVERT: M 86 LYS cc_start: 0.7743 (mttt) cc_final: 0.6888 (mtpp) REVERT: M 104 ARG cc_start: 0.7437 (ttm170) cc_final: 0.7178 (ttp-170) REVERT: M 124 MET cc_start: 0.8972 (mtm) cc_final: 0.8735 (mtp) REVERT: M 190 GLU cc_start: 0.8008 (tp30) cc_final: 0.7557 (tp30) REVERT: M 227 GLN cc_start: 0.7126 (pm20) cc_final: 0.6805 (pm20) REVERT: M 300 PHE cc_start: 0.7945 (m-80) cc_final: 0.7743 (m-80) REVERT: O 229 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8030 (tp-100) REVERT: R 122 GLU cc_start: 0.3430 (mm-30) cc_final: 0.2850 (mm-30) REVERT: R 145 LEU cc_start: 0.8360 (mm) cc_final: 0.7559 (mt) REVERT: R 181 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8419 (tp-100) REVERT: U 358 MET cc_start: 0.6876 (ppp) cc_final: 0.6113 (ppp) outliers start: 69 outliers final: 45 residues processed: 658 average time/residue: 0.5153 time to fit residues: 410.6807 Evaluate side-chains 652 residues out of total 4684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 595 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1052 ARG Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1327 GLU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 303 ASP Chi-restraints excluded: chain O residue 191 GLU Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 115 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 337 optimal weight: 1.9990 chunk 97 optimal weight: 0.0980 chunk 279 optimal weight: 0.9990 chunk 429 optimal weight: 1.9990 chunk 207 optimal weight: 0.3980 chunk 523 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 349 optimal weight: 2.9990 chunk 412 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 389 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN I 22 ASN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN V 35 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.207507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.122910 restraints weight = 46803.714| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.24 r_work: 0.3069 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.366 45270 Z= 0.175 Angle : 0.647 59.200 61482 Z= 0.340 Chirality : 0.042 0.392 6849 Planarity : 0.004 0.062 7660 Dihedral : 12.280 59.900 6734 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.49 % Allowed : 16.99 % Favored : 81.51 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.12), residues: 5233 helix: 1.29 (0.12), residues: 1977 sheet: 0.25 (0.18), residues: 819 loop : -0.06 (0.13), residues: 2437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 241 TYR 0.025 0.001 TYR B 648 PHE 0.019 0.001 PHE A 397 TRP 0.021 0.002 TRP A1334 HIS 0.032 0.001 HIS R 182 Details of bonding type rmsd covalent geometry : bond 0.00391 (45231) covalent geometry : angle 0.63180 (61434) hydrogen bonds : bond 0.03684 ( 1201) hydrogen bonds : angle 3.68369 ( 3431) metal coordination : bond 0.01433 ( 39) metal coordination : angle 5.00268 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23440.12 seconds wall clock time: 397 minutes 0.63 seconds (23820.63 seconds total)