Starting phenix.real_space_refine on Sat Mar 7 11:07:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z1m_14448/03_2026/7z1m_14448.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z1m_14448/03_2026/7z1m_14448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z1m_14448/03_2026/7z1m_14448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z1m_14448/03_2026/7z1m_14448.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z1m_14448/03_2026/7z1m_14448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z1m_14448/03_2026/7z1m_14448.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 7 6.06 5 P 53 5.49 5 Mg 1 5.21 5 S 218 5.16 5 C 26533 2.51 5 N 7263 2.21 5 O 8047 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42122 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1436, 11231 Classifications: {'peptide': 1436} Link IDs: {'PTRANS': 66, 'TRANS': 1369} Chain breaks: 2 Chain: "B" Number of atoms: 8693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8693 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 41, 'TRANS': 1059} Chain breaks: 1 Chain: "C" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2647 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "D" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1185 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1610 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain breaks: 1 Chain: "H" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1083 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 1 Chain: "I" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 872 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 801 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain breaks: 1 Chain: "N" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1171 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain breaks: 2 Chain: "O" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4577 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 20, 'TRANS': 549} Chain breaks: 1 Chain: "P" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1162 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "Q" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 8, 'TRANS': 114} Chain breaks: 1 Chain: "R" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 172 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna3p': 7} Chain: "S" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "T" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 578 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '4QM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'4QM': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 500 SG CYS A 67 113.988 78.063 107.654 1.00103.78 S ATOM 518 SG CYS A 70 112.881 74.451 107.042 1.00 98.55 S ATOM 565 SG CYS A 77 111.227 77.398 105.146 1.00 94.29 S ATOM 803 SG CYS A 107 82.546 99.044 137.789 1.00 94.17 S ATOM 826 SG CYS A 110 83.424 96.005 139.954 1.00 94.94 S ATOM 1192 SG CYS A 154 79.865 97.074 139.637 1.00104.66 S ATOM 1216 SG CYS A 157 82.310 99.093 141.702 1.00103.18 S ATOM 19497 SG CYS B1095 99.467 69.121 117.110 1.00 88.46 S ATOM 19520 SG CYS B1098 98.875 72.818 117.497 1.00 85.02 S ATOM 19586 SG CYS B1107 102.372 71.632 116.924 1.00 91.15 S ATOM 19606 SG CYS B1110 100.775 70.817 120.233 1.00 95.02 S ATOM 28918 SG CYS I 5 61.534 152.241 107.302 1.00148.90 S ATOM 28937 SG CYS I 8 65.165 151.369 107.468 1.00149.54 S ATOM 29065 SG CYS I 26 63.010 149.978 110.253 1.00150.50 S ATOM 29088 SG CYS I 29 63.701 153.655 110.055 1.00157.64 S ATOM 29463 SG CYS I 75 13.698 124.762 98.587 1.00246.69 S ATOM 29665 SG CYS I 100 14.919 122.695 96.536 1.00237.06 S ATOM 29686 SG CYS I 103 17.084 124.999 98.348 1.00240.25 S ATOM 29805 SG CYS J 7 93.837 90.248 38.579 1.00 83.27 S ATOM 29828 SG CYS J 10 93.351 87.552 35.887 1.00 81.74 S ATOM 30108 SG CYS J 45 90.573 90.010 36.850 1.00 85.95 S ATOM 30114 SG CYS J 46 93.665 90.897 34.690 1.00 84.92 S ATOM 31171 SG CYS L 31 127.397 109.298 58.754 1.00104.55 S ATOM 31191 SG CYS L 34 129.239 110.075 55.649 1.00106.37 S ATOM 31295 SG CYS L 48 131.281 109.469 58.626 1.00112.53 S ATOM 31318 SG CYS L 51 129.227 112.670 58.528 1.00113.33 S Time building chain proxies: 9.31, per 1000 atoms: 0.22 Number of scatterers: 42122 At special positions: 0 Unit cell: (148.863, 193.626, 197.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 218 16.00 P 53 15.00 Mg 1 11.99 O 8047 8.00 N 7263 7.00 C 26533 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 67 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 77 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 70 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 110 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 157 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 107 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1098 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1110 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 26 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 100 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 100 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " Number of angles added : 33 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9718 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 50 sheets defined 41.5% alpha, 14.1% beta 16 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 5.34 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 73 through 77 removed outlier: 4.055A pdb=" N CYS A 77 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 133 through 151 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 191 through 206 Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.778A pdb=" N GLN A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 283 through 306 Processing helix chain 'A' and resid 308 through 328 Processing helix chain 'A' and resid 329 through 332 removed outlier: 3.789A pdb=" N VAL A 332 " --> pdb=" O SER A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.843A pdb=" N TYR A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.942A pdb=" N LEU A 541 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.646A pdb=" N SER A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 615 Processing helix chain 'A' and resid 642 through 646 Processing helix chain 'A' and resid 676 through 705 Proline residue: A 687 - end of helix removed outlier: 3.968A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 705 " --> pdb=" O CYS A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 717 Processing helix chain 'A' and resid 722 through 748 removed outlier: 3.723A pdb=" N GLU A 728 " --> pdb=" O LYS A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 784 Processing helix chain 'A' and resid 789 through 798 Processing helix chain 'A' and resid 802 through 811 Processing helix chain 'A' and resid 841 through 846 Processing helix chain 'A' and resid 857 through 894 removed outlier: 4.420A pdb=" N THR A 879 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.640A pdb=" N ASP A 919 " --> pdb=" O TYR A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 946 Processing helix chain 'A' and resid 955 through 973 Proline residue: A 969 - end of helix removed outlier: 3.568A pdb=" N ARG A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1025 removed outlier: 3.970A pdb=" N LEU A1022 " --> pdb=" O ALA A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1060 Processing helix chain 'A' and resid 1063 through 1081 Processing helix chain 'A' and resid 1088 through 1099 Processing helix chain 'A' and resid 1099 through 1104 removed outlier: 3.957A pdb=" N GLN A1103 " --> pdb=" O GLU A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1131 Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.596A pdb=" N ARG A1160 " --> pdb=" O VAL A1156 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A1161 " --> pdb=" O VAL A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1169 No H-bonds generated for 'chain 'A' and resid 1167 through 1169' Processing helix chain 'A' and resid 1189 through 1197 removed outlier: 3.945A pdb=" N ILE A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1211 Processing helix chain 'A' and resid 1254 through 1267 removed outlier: 3.607A pdb=" N TYR A1258 " --> pdb=" O ASN A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1306 Processing helix chain 'A' and resid 1318 through 1346 removed outlier: 3.865A pdb=" N VAL A1322 " --> pdb=" O HIS A1318 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ILE A1328 " --> pdb=" O SER A1324 " (cutoff:3.500A) removed outlier: 9.524A pdb=" N GLU A1329 " --> pdb=" O VAL A1325 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A1330 " --> pdb=" O LEU A1326 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS A1346 " --> pdb=" O THR A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1363 removed outlier: 3.984A pdb=" N ILE A1355 " --> pdb=" O ASP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1380 removed outlier: 3.689A pdb=" N SER A1377 " --> pdb=" O ARG A1373 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A1378 " --> pdb=" O PHE A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1390 removed outlier: 3.521A pdb=" N LEU A1386 " --> pdb=" O SER A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1403 Processing helix chain 'A' and resid 1411 through 1418 Processing helix chain 'A' and resid 1423 through 1427 Processing helix chain 'A' and resid 1437 through 1441 Processing helix chain 'A' and resid 1446 through 1452 Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.664A pdb=" N ASP B 43 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TRP B 45 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.861A pdb=" N ALA B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 80 removed outlier: 3.510A pdb=" N LEU B 62 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 264 through 273 removed outlier: 3.569A pdb=" N ILE B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 293 removed outlier: 3.947A pdb=" N GLN B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 290 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 318 through 329 Processing helix chain 'B' and resid 342 through 362 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 408 removed outlier: 3.564A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 422 through 440 removed outlier: 4.282A pdb=" N ASN B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.769A pdb=" N MET B 470 " --> pdb=" O ALA B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 removed outlier: 3.553A pdb=" N GLN B 493 " --> pdb=" O GLN B 490 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE B 494 " --> pdb=" O PRO B 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 490 through 494' Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'B' and resid 542 through 544 No H-bonds generated for 'chain 'B' and resid 542 through 544' Processing helix chain 'B' and resid 548 through 552 removed outlier: 3.860A pdb=" N ASN B 552 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 582 Processing helix chain 'B' and resid 623 through 633 removed outlier: 3.534A pdb=" N GLY B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 643 Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.805A pdb=" N ASP B 656 " --> pdb=" O ASN B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 681 removed outlier: 3.857A pdb=" N THR B 679 " --> pdb=" O GLU B 676 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 681 " --> pdb=" O PHE B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 688 Processing helix chain 'B' and resid 690 through 694 Processing helix chain 'B' and resid 695 through 706 Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 738 through 744 Processing helix chain 'B' and resid 763 through 767 removed outlier: 3.854A pdb=" N ASP B 766 " --> pdb=" O SER B 763 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE B 767 " --> pdb=" O GLY B 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 763 through 767' Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 818 through 822 Processing helix chain 'B' and resid 947 through 953 removed outlier: 4.457A pdb=" N SER B 951 " --> pdb=" O HIS B 947 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 952 " --> pdb=" O GLY B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 971 removed outlier: 3.988A pdb=" N MET B 958 " --> pdb=" O THR B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 995 removed outlier: 3.640A pdb=" N MET B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1034 Processing helix chain 'B' and resid 1053 through 1057 Processing helix chain 'B' and resid 1063 through 1074 Processing helix chain 'B' and resid 1075 through 1084 Processing helix chain 'B' and resid 1123 through 1135 Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.508A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 157 removed outlier: 3.750A pdb=" N TYR C 157 " --> pdb=" O PRO C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.648A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.548A pdb=" N PHE C 285 " --> pdb=" O TYR C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 331 Processing helix chain 'D' and resid 12 through 28 Processing helix chain 'D' and resid 30 through 38 Processing helix chain 'D' and resid 52 through 68 Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 99 through 112 removed outlier: 4.420A pdb=" N SER D 112 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 127 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 146 through 159 Processing helix chain 'E' and resid 2 through 26 removed outlier: 4.191A pdb=" N ARG E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASN E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.551A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.740A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.599A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.762A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.527A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 162 through 175 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.992A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.270A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 removed outlier: 4.109A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.805A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 4.230A pdb=" N LYS J 59 " --> pdb=" O ASP J 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 82 removed outlier: 4.539A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.842A pdb=" N ALA K 116 " --> pdb=" O THR K 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 140 removed outlier: 4.315A pdb=" N ALA M 136 " --> pdb=" O ASN M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 200 removed outlier: 3.573A pdb=" N ASP M 187 " --> pdb=" O PHE M 183 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG M 200 " --> pdb=" O GLU M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 240 removed outlier: 3.985A pdb=" N ALA M 233 " --> pdb=" O GLY M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 251 through 265 removed outlier: 4.383A pdb=" N ASP M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 274 through 279 removed outlier: 3.804A pdb=" N ILE M 278 " --> pdb=" O GLN M 274 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP M 279 " --> pdb=" O GLU M 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 274 through 279' Processing helix chain 'N' and resid 215 through 224 removed outlier: 3.891A pdb=" N LEU N 223 " --> pdb=" O ILE N 219 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER N 224 " --> pdb=" O GLN N 220 " (cutoff:3.500A) Processing helix chain 'N' and resid 274 through 297 Processing helix chain 'O' and resid 27 through 35 Processing helix chain 'O' and resid 38 through 42 removed outlier: 3.544A pdb=" N THR O 41 " --> pdb=" O GLU O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 57 Processing helix chain 'O' and resid 58 through 72 Processing helix chain 'O' and resid 76 through 83 Processing helix chain 'O' and resid 87 through 101 removed outlier: 3.683A pdb=" N LEU O 101 " --> pdb=" O SER O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 132 removed outlier: 3.943A pdb=" N ILE O 127 " --> pdb=" O ASN O 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 144 removed outlier: 3.669A pdb=" N MET O 144 " --> pdb=" O ILE O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 167 Processing helix chain 'O' and resid 171 through 176 Processing helix chain 'O' and resid 180 through 198 Processing helix chain 'O' and resid 204 through 209 Processing helix chain 'O' and resid 210 through 225 Processing helix chain 'O' and resid 233 through 254 removed outlier: 3.650A pdb=" N ASN O 254 " --> pdb=" O ALA O 250 " (cutoff:3.500A) Processing helix chain 'O' and resid 255 through 259 removed outlier: 4.217A pdb=" N LEU O 259 " --> pdb=" O PRO O 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 283 through 301 removed outlier: 3.619A pdb=" N PHE O 287 " --> pdb=" O ASN O 283 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 319 removed outlier: 3.732A pdb=" N GLN O 310 " --> pdb=" O SER O 306 " (cutoff:3.500A) Processing helix chain 'O' and resid 328 through 337 removed outlier: 3.807A pdb=" N GLY O 334 " --> pdb=" O THR O 331 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU O 335 " --> pdb=" O GLN O 332 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU O 336 " --> pdb=" O THR O 333 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN O 337 " --> pdb=" O GLY O 334 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 356 removed outlier: 3.642A pdb=" N GLU O 353 " --> pdb=" O ALA O 349 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU O 354 " --> pdb=" O GLU O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 364 through 370 removed outlier: 4.086A pdb=" N ARG O 368 " --> pdb=" O ILE O 364 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N HIS O 369 " --> pdb=" O ASP O 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 449 through 462 Processing helix chain 'O' and resid 479 through 514 Proline residue: O 485 - end of helix Proline residue: O 502 - end of helix removed outlier: 3.670A pdb=" N MET O 505 " --> pdb=" O GLY O 501 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 526 Processing helix chain 'O' and resid 529 through 542 removed outlier: 4.224A pdb=" N ARG O 542 " --> pdb=" O ALA O 538 " (cutoff:3.500A) Processing helix chain 'O' and resid 558 through 560 No H-bonds generated for 'chain 'O' and resid 558 through 560' Processing helix chain 'O' and resid 569 through 599 removed outlier: 3.534A pdb=" N SER O 573 " --> pdb=" O LYS O 569 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN O 599 " --> pdb=" O LEU O 595 " (cutoff:3.500A) Processing helix chain 'O' and resid 599 through 607 Processing helix chain 'O' and resid 614 through 619 Processing helix chain 'O' and resid 620 through 649 Processing helix chain 'P' and resid 171 through 191 Processing helix chain 'P' and resid 193 through 197 Processing helix chain 'P' and resid 217 through 228 Processing helix chain 'P' and resid 236 through 250 removed outlier: 3.542A pdb=" N ASP P 250 " --> pdb=" O VAL P 246 " (cutoff:3.500A) Processing helix chain 'P' and resid 264 through 271 removed outlier: 3.635A pdb=" N ILE P 268 " --> pdb=" O THR P 264 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 67 Processing helix chain 'Q' and resid 128 through 132 removed outlier: 3.800A pdb=" N PHE Q 132 " --> pdb=" O LEU Q 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 137 Processing sheet with id=AA1, first strand: chain 'A' and resid 1405 through 1407 removed outlier: 6.664A pdb=" N ARG B1142 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU A 16 " --> pdb=" O ARG B1140 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG B1140 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 33 removed outlier: 4.362A pdb=" N SER A 30 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS A 83 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL A 32 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LYS A 85 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 86 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARG A 259 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.543A pdb=" N LEU A 88 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N ILE A 257 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 40 through 41 removed outlier: 4.072A pdb=" N ALA A 47 " --> pdb=" O ASP A 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 166 removed outlier: 4.424A pdb=" N ILE A 178 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 372 Processing sheet with id=AA6, first strand: chain 'B' and resid 1036 through 1037 removed outlier: 3.734A pdb=" N LEU A 500 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 403 through 407 removed outlier: 3.941A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N HIS A 465 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA A 430 " --> pdb=" O HIS A 465 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA9, first strand: chain 'A' and resid 626 through 629 removed outlier: 6.184A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 814 through 815 removed outlier: 3.670A pdb=" N GLY A 814 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 848 " --> pdb=" O GLY A 814 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 897 through 898 removed outlier: 7.102A pdb=" N VAL A 904 " --> pdb=" O VAL A 912 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1281 through 1285 Processing sheet with id=AB4, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 3.854A pdb=" N LYS A1273 " --> pdb=" O THR A1164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1222 through 1225 removed outlier: 4.209A pdb=" N TYR A1172 " --> pdb=" O ARG A1187 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A1173 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE I 40 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1429 through 1432 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1429 through 1432 current: chain 'F' and resid 145 through 147 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 145 through 147 current: chain 'G' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 43 through 54 current: chain 'G' and resid 66 through 77 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 82 through 84 removed outlier: 7.728A pdb=" N LEU B 93 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N THR B 136 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TYR B 95 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU B 134 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP B 97 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA B 127 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY B 150 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE B 129 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU B 148 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL B 131 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP B 146 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB9, first strand: chain 'B' and resid 375 through 378 removed outlier: 6.826A pdb=" N VAL B 196 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 205 through 210 removed outlier: 4.770A pdb=" N VAL B 216 " --> pdb=" O THR B 235 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 442 through 444 Processing sheet with id=AC3, first strand: chain 'B' and resid 519 through 520 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 619 through 620 current: chain 'B' and resid 672 through 673 Processing sheet with id=AC4, first strand: chain 'B' and resid 539 through 540 removed outlier: 6.680A pdb=" N VAL B 555 " --> pdb=" O ILE B 562 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 724 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 785 through 795 current: chain 'B' and resid 879 through 888 removed outlier: 6.625A pdb=" N LEU B 899 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL B 884 " --> pdb=" O LYS B 897 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS B 897 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N MET B 886 " --> pdb=" O LEU B 895 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU B 895 " --> pdb=" O MET B 886 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 894 through 904 current: chain 'L' and resid 37 through 38 Processing sheet with id=AC6, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AC7, first strand: chain 'B' and resid 753 through 759 removed outlier: 4.167A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 911 through 912 removed outlier: 7.618A pdb=" N LEU B 773 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE B 925 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 841 through 843 removed outlier: 4.020A pdb=" N ILE B 843 " --> pdb=" O VAL B 871 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 846 through 848 Processing sheet with id=AD2, first strand: chain 'B' and resid 1101 through 1102 removed outlier: 4.263A pdb=" N ASP B1093 " --> pdb=" O GLY B1102 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.502A pdb=" N THR C 13 " --> pdb=" O GLY C 6 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 12 through 13 current: chain 'C' and resid 51 through 57 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 57 current: chain 'C' and resid 289 through 304 Processing sheet with id=AD4, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.248A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AD6, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AD7, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.430A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 87 through 88 removed outlier: 3.751A pdb=" N VAL E 88 " --> pdb=" O ASN E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.915A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 84 through 92 removed outlier: 5.323A pdb=" N ILE G 89 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N SER G 100 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE G 108 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY G 198 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG G 152 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER G 199 " --> pdb=" O ILE G 150 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE G 150 " --> pdb=" O SER G 199 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AE3, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.822A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA H 60 " --> pdb=" O TYR H 141 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 13 through 15 Processing sheet with id=AE5, first strand: chain 'I' and resid 64 through 66 Processing sheet with id=AE6, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AE7, first strand: chain 'M' and resid 70 through 75 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 70 through 75 current: chain 'M' and resid 118 through 124 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 145 through 154 current: chain 'M' and resid 167 through 182 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 167 through 182 current: chain 'N' and resid 371 through 375 removed outlier: 6.798A pdb=" N LEU N 371 " --> pdb=" O ILE N 382 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE N 382 " --> pdb=" O LEU N 371 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 378 through 383 current: chain 'N' and resid 405 through 420 Processing sheet with id=AE8, first strand: chain 'M' and resid 96 through 97 Processing sheet with id=AE9, first strand: chain 'O' and resid 74 through 75 Processing sheet with id=AF1, first strand: chain 'O' and resid 168 through 170 Processing sheet with id=AF2, first strand: chain 'O' and resid 380 through 381 Processing sheet with id=AF3, first strand: chain 'O' and resid 516 through 517 Processing sheet with id=AF4, first strand: chain 'P' and resid 165 through 166 Processing sheet with id=AF5, first strand: chain 'P' and resid 253 through 257 removed outlier: 3.936A pdb=" N VAL P 256 " --> pdb=" O CYS P 260 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N CYS P 260 " --> pdb=" O VAL P 256 " (cutoff:3.500A) 1656 hydrogen bonds defined for protein. 4632 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 11.15 Time building geometry restraints manager: 4.78 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: 13451 1.34 - 1.46: 8168 1.46 - 1.58: 20913 1.58 - 1.70: 111 1.70 - 1.82: 354 Bond restraints: 42997 Sorted by residual: bond pdb=" C15 4QM A2003 " pdb=" C16 4QM A2003 " ideal model delta sigma weight residual 1.529 1.598 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C15 4QM C 401 " pdb=" C16 4QM C 401 " ideal model delta sigma weight residual 1.529 1.592 -0.063 2.00e-02 2.50e+03 9.88e+00 bond pdb=" C19 4QM C 401 " pdb=" C2 4QM C 401 " ideal model delta sigma weight residual 1.551 1.612 -0.061 2.00e-02 2.50e+03 9.32e+00 bond pdb=" C16 4QM C 401 " pdb=" C17 4QM C 401 " ideal model delta sigma weight residual 1.527 1.586 -0.059 2.00e-02 2.50e+03 8.72e+00 bond pdb=" C16 4QM A2003 " pdb=" C17 4QM A2003 " ideal model delta sigma weight residual 1.527 1.585 -0.058 2.00e-02 2.50e+03 8.54e+00 ... (remaining 42992 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 57816 2.98 - 5.95: 400 5.95 - 8.93: 65 8.93 - 11.91: 15 11.91 - 14.88: 1 Bond angle restraints: 58297 Sorted by residual: angle pdb=" N ILE A 550 " pdb=" CA ILE A 550 " pdb=" C ILE A 550 " ideal model delta sigma weight residual 113.71 107.60 6.11 9.50e-01 1.11e+00 4.13e+01 angle pdb=" N PRO E 128 " pdb=" CA PRO E 128 " pdb=" C PRO E 128 " ideal model delta sigma weight residual 110.70 117.05 -6.35 1.22e+00 6.72e-01 2.71e+01 angle pdb=" CA PRO E 128 " pdb=" C PRO E 128 " pdb=" N PRO E 129 " ideal model delta sigma weight residual 117.93 123.98 -6.05 1.20e+00 6.94e-01 2.55e+01 angle pdb=" N GLU D 155 " pdb=" CA GLU D 155 " pdb=" CB GLU D 155 " ideal model delta sigma weight residual 110.30 117.66 -7.36 1.54e+00 4.22e-01 2.28e+01 angle pdb=" CA ARG O 145 " pdb=" CB ARG O 145 " pdb=" CG ARG O 145 " ideal model delta sigma weight residual 114.10 123.34 -9.24 2.00e+00 2.50e-01 2.13e+01 ... (remaining 58292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.29: 25000 27.29 - 54.57: 1204 54.57 - 81.86: 140 81.86 - 109.15: 25 109.15 - 136.43: 1 Dihedral angle restraints: 26370 sinusoidal: 11348 harmonic: 15022 Sorted by residual: dihedral pdb=" CA ASP O 266 " pdb=" C ASP O 266 " pdb=" N PRO O 267 " pdb=" CA PRO O 267 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ASN O 514 " pdb=" C ASN O 514 " pdb=" N LYS O 515 " pdb=" CA LYS O 515 " ideal model delta harmonic sigma weight residual -180.00 -157.84 -22.16 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ARG B 313 " pdb=" C ARG B 313 " pdb=" N ARG B 314 " pdb=" CA ARG B 314 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 26367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 5775 0.071 - 0.142: 761 0.142 - 0.213: 33 0.213 - 0.284: 8 0.284 - 0.355: 4 Chirality restraints: 6581 Sorted by residual: chirality pdb=" C9 4QM C 401 " pdb=" C20 4QM C 401 " pdb=" C5 4QM C 401 " pdb=" C8 4QM C 401 " both_signs ideal model delta sigma weight residual False 2.61 2.97 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C17 4QM A2003 " pdb=" C16 4QM A2003 " pdb=" C18 4QM A2003 " pdb=" O3 4QM A2003 " both_signs ideal model delta sigma weight residual False 2.39 2.70 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C17 4QM C 401 " pdb=" C16 4QM C 401 " pdb=" C18 4QM C 401 " pdb=" O3 4QM C 401 " both_signs ideal model delta sigma weight residual False 2.39 2.70 -0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 6578 not shown) Planarity restraints: 7312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU I 92 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO I 93 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO I 93 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO I 93 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 127 " -0.042 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO E 128 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO E 128 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 128 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A1006 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C HIS A1006 " 0.034 2.00e-02 2.50e+03 pdb=" O HIS A1006 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A1007 " -0.012 2.00e-02 2.50e+03 ... (remaining 7309 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 569 2.66 - 3.22: 38253 3.22 - 3.78: 64930 3.78 - 4.34: 87380 4.34 - 4.90: 145054 Nonbonded interactions: 336186 Sorted by model distance: nonbonded pdb=" OD1 ASP A 511 " pdb="MG MG A2002 " model vdw 2.100 2.170 nonbonded pdb=" O ILE Q 122 " pdb=" OH TYR Q 127 " model vdw 2.195 3.040 nonbonded pdb=" OG SER A 980 " pdb=" OE2 GLU E 160 " model vdw 2.200 3.040 nonbonded pdb=" O PHE C 86 " pdb=" OG SER C 203 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR B 231 " pdb=" O VAL B 331 " model vdw 2.226 3.040 ... (remaining 336181 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=0.00 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: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 49.030 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 0.069 43025 Z= 0.175 Angle : 0.698 14.884 58330 Z= 0.361 Chirality : 0.047 0.355 6581 Planarity : 0.005 0.067 7312 Dihedral : 15.315 136.435 16652 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.30 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.11), residues: 5095 helix: 0.71 (0.12), residues: 1889 sheet: -0.26 (0.19), residues: 722 loop : -0.88 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 227 TYR 0.032 0.001 TYR I 98 PHE 0.032 0.001 PHE B1018 TRP 0.026 0.002 TRP G 211 HIS 0.005 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00381 (42997) covalent geometry : angle 0.69268 (58297) hydrogen bonds : bond 0.14503 ( 1692) hydrogen bonds : angle 5.80168 ( 4704) metal coordination : bond 0.00550 ( 27) metal coordination : angle 3.53209 ( 33) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 503 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 736 HIS cc_start: 0.7635 (t-90) cc_final: 0.7349 (t-90) REVERT: A 1165 LEU cc_start: 0.8697 (mt) cc_final: 0.8196 (mt) REVERT: A 1259 ARG cc_start: 0.7977 (ttt90) cc_final: 0.7690 (tpt170) REVERT: C 240 LYS cc_start: 0.8361 (mmtt) cc_final: 0.8103 (mmtm) REVERT: C 287 ASP cc_start: 0.8383 (m-30) cc_final: 0.8036 (t0) REVERT: D 135 TYR cc_start: 0.8369 (m-80) cc_final: 0.8055 (m-80) REVERT: F 110 ASP cc_start: 0.8120 (p0) cc_final: 0.7758 (p0) REVERT: G 114 MET cc_start: 0.8119 (mtm) cc_final: 0.7826 (mtm) REVERT: G 120 TYR cc_start: 0.7975 (p90) cc_final: 0.7660 (p90) REVERT: K 129 ASP cc_start: 0.8481 (t70) cc_final: 0.8194 (t0) REVERT: M 77 LYS cc_start: 0.6937 (tttt) cc_final: 0.6729 (tttt) REVERT: M 112 TYR cc_start: 0.7526 (t80) cc_final: 0.6403 (t80) REVERT: M 254 GLN cc_start: 0.8695 (mp10) cc_final: 0.8438 (mp10) REVERT: O 261 GLN cc_start: 0.8580 (mp10) cc_final: 0.8271 (mp10) REVERT: O 629 MET cc_start: 0.7826 (mpp) cc_final: 0.7478 (mpp) REVERT: P 225 ILE cc_start: 0.8507 (tp) cc_final: 0.8229 (tp) REVERT: P 251 ASP cc_start: 0.8893 (t0) cc_final: 0.8621 (t0) REVERT: P 269 LEU cc_start: 0.8786 (mm) cc_final: 0.8550 (mt) REVERT: Q 51 GLU cc_start: 0.8691 (mp0) cc_final: 0.8404 (mp0) outliers start: 0 outliers final: 0 residues processed: 503 average time/residue: 0.2616 time to fit residues: 215.5696 Evaluate side-chains 444 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 394 optimal weight: 10.0000 chunk 430 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 265 optimal weight: 2.9990 chunk 497 optimal weight: 3.9990 chunk 414 optimal weight: 10.0000 chunk 310 optimal weight: 6.9990 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 134 ASN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN A1185 GLN B 693 HIS B 821 HIS B1115 ASN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN ** N 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 ASN O 193 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.070315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.052110 restraints weight = 119258.460| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.64 r_work: 0.2750 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 43025 Z= 0.401 Angle : 0.741 19.185 58330 Z= 0.378 Chirality : 0.048 0.180 6581 Planarity : 0.005 0.057 7312 Dihedral : 10.695 140.273 6340 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.55 % Favored : 95.43 % Rotamer: Outliers : 0.77 % Allowed : 7.73 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.12), residues: 5095 helix: 1.11 (0.12), residues: 1898 sheet: -0.39 (0.19), residues: 730 loop : -0.92 (0.12), residues: 2467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 55 TYR 0.038 0.002 TYR B 416 PHE 0.033 0.002 PHE A 474 TRP 0.020 0.002 TRP A 201 HIS 0.016 0.002 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00917 (42997) covalent geometry : angle 0.72948 (58297) hydrogen bonds : bond 0.04915 ( 1692) hydrogen bonds : angle 4.80867 ( 4704) metal coordination : bond 0.01627 ( 27) metal coordination : angle 5.58908 ( 33) Misc. bond : bond 0.00108 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 457 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 736 HIS cc_start: 0.7844 (t-90) cc_final: 0.7573 (t-90) REVERT: A 1172 TYR cc_start: 0.8212 (p90) cc_final: 0.7048 (p90) REVERT: B 123 MET cc_start: 0.8861 (mtt) cc_final: 0.8645 (mtt) REVERT: B 800 ASN cc_start: 0.8593 (t0) cc_final: 0.8162 (t0) REVERT: C 240 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8337 (mmtt) REVERT: D 21 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8971 (t) REVERT: D 60 ARG cc_start: 0.9026 (tpp-160) cc_final: 0.8305 (tpm170) REVERT: D 64 ASN cc_start: 0.8725 (m-40) cc_final: 0.7997 (m-40) REVERT: D 98 MET cc_start: 0.8101 (ptm) cc_final: 0.7303 (ppp) REVERT: D 107 MET cc_start: 0.9134 (mmm) cc_final: 0.8900 (mmm) REVERT: D 135 TYR cc_start: 0.8512 (m-80) cc_final: 0.7887 (m-80) REVERT: D 149 THR cc_start: 0.8134 (p) cc_final: 0.7835 (p) REVERT: E 122 LYS cc_start: 0.8515 (pttp) cc_final: 0.7537 (pttp) REVERT: F 110 ASP cc_start: 0.8513 (p0) cc_final: 0.8114 (p0) REVERT: G 112 GLN cc_start: 0.8300 (tp-100) cc_final: 0.8089 (mm-40) REVERT: G 114 MET cc_start: 0.8197 (mtm) cc_final: 0.7941 (mtm) REVERT: G 120 TYR cc_start: 0.8037 (p90) cc_final: 0.7779 (p90) REVERT: G 130 TRP cc_start: 0.7416 (t60) cc_final: 0.7116 (t60) REVERT: H 45 GLU cc_start: 0.9134 (tt0) cc_final: 0.8868 (tm-30) REVERT: H 52 GLN cc_start: 0.9369 (mm-40) cc_final: 0.9105 (mm-40) REVERT: I 43 ARG cc_start: 0.8670 (ttm170) cc_final: 0.7845 (ttm170) REVERT: K 87 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8318 (tm-30) REVERT: K 129 ASP cc_start: 0.8894 (t70) cc_final: 0.8692 (t0) REVERT: K 137 GLU cc_start: 0.8556 (tp30) cc_final: 0.8334 (tp30) REVERT: M 77 LYS cc_start: 0.7320 (tttt) cc_final: 0.7002 (tttt) REVERT: M 112 TYR cc_start: 0.7597 (t80) cc_final: 0.6944 (t80) REVERT: M 254 GLN cc_start: 0.8711 (mp10) cc_final: 0.8383 (mp10) REVERT: O 144 MET cc_start: 0.8615 (ptm) cc_final: 0.8255 (ttp) REVERT: O 261 GLN cc_start: 0.8593 (mp10) cc_final: 0.8272 (mp10) REVERT: P 225 ILE cc_start: 0.8724 (tp) cc_final: 0.8475 (tp) REVERT: P 251 ASP cc_start: 0.8952 (t0) cc_final: 0.8591 (t0) REVERT: Q 15 TYR cc_start: 0.6340 (t80) cc_final: 0.5880 (t80) REVERT: Q 16 MET cc_start: 0.6867 (OUTLIER) cc_final: 0.6531 (mmp) REVERT: Q 51 GLU cc_start: 0.8969 (mp0) cc_final: 0.8575 (mp0) outliers start: 35 outliers final: 22 residues processed: 470 average time/residue: 0.2640 time to fit residues: 205.6974 Evaluate side-chains 458 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 434 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1217 ILE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 36 CYS Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain P residue 171 ASP Chi-restraints excluded: chain P residue 292 SER Chi-restraints excluded: chain Q residue 16 MET Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 131 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 217 optimal weight: 2.9990 chunk 454 optimal weight: 8.9990 chunk 341 optimal weight: 5.9990 chunk 309 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 414 optimal weight: 10.0000 chunk 313 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 488 optimal weight: 9.9990 chunk 435 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 311 ASN A 941 HIS C 32 ASN D 47 ASN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.071300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.053210 restraints weight = 117405.493| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.60 r_work: 0.2780 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 43025 Z= 0.245 Angle : 0.601 14.843 58330 Z= 0.309 Chirality : 0.044 0.157 6581 Planarity : 0.004 0.052 7312 Dihedral : 10.636 142.025 6340 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.69 % Favored : 96.29 % Rotamer: Outliers : 1.27 % Allowed : 10.05 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.12), residues: 5095 helix: 1.36 (0.12), residues: 1895 sheet: -0.36 (0.19), residues: 728 loop : -0.86 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 227 TYR 0.024 0.002 TYR B1024 PHE 0.027 0.001 PHE A 474 TRP 0.017 0.002 TRP A 201 HIS 0.010 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00561 (42997) covalent geometry : angle 0.59201 (58297) hydrogen bonds : bond 0.04240 ( 1692) hydrogen bonds : angle 4.56140 ( 4704) metal coordination : bond 0.01087 ( 27) metal coordination : angle 4.49896 ( 33) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 465 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 736 HIS cc_start: 0.7787 (t-90) cc_final: 0.7505 (t-90) REVERT: A 1117 MET cc_start: 0.8035 (mmm) cc_final: 0.7317 (mmp) REVERT: A 1172 TYR cc_start: 0.8147 (p90) cc_final: 0.6747 (p90) REVERT: A 1348 MET cc_start: 0.8928 (mmt) cc_final: 0.8711 (mmt) REVERT: B 351 MET cc_start: 0.8726 (mmp) cc_final: 0.8372 (mmp) REVERT: B 800 ASN cc_start: 0.8591 (t0) cc_final: 0.8129 (t0) REVERT: B 885 MET cc_start: 0.8666 (tmm) cc_final: 0.8266 (tmm) REVERT: C 240 LYS cc_start: 0.8633 (mmtt) cc_final: 0.8280 (mmtt) REVERT: D 13 ASP cc_start: 0.8859 (m-30) cc_final: 0.8186 (m-30) REVERT: D 60 ARG cc_start: 0.9047 (tpp-160) cc_final: 0.8796 (tpp-160) REVERT: D 98 MET cc_start: 0.8160 (ptm) cc_final: 0.7392 (ppp) REVERT: D 125 ASN cc_start: 0.8179 (m-40) cc_final: 0.7978 (m-40) REVERT: D 135 TYR cc_start: 0.8506 (m-80) cc_final: 0.7833 (m-80) REVERT: E 122 LYS cc_start: 0.8491 (pttp) cc_final: 0.7510 (pttp) REVERT: G 114 MET cc_start: 0.8185 (mtm) cc_final: 0.7942 (mtm) REVERT: G 120 TYR cc_start: 0.8106 (p90) cc_final: 0.7874 (p90) REVERT: G 130 TRP cc_start: 0.7347 (t60) cc_final: 0.7099 (t60) REVERT: H 45 GLU cc_start: 0.9114 (tt0) cc_final: 0.8834 (tm-30) REVERT: H 52 GLN cc_start: 0.9432 (mm-40) cc_final: 0.9136 (mm-40) REVERT: H 83 GLN cc_start: 0.8188 (mp10) cc_final: 0.7980 (mp10) REVERT: I 43 ARG cc_start: 0.8552 (ttm170) cc_final: 0.7634 (ttm170) REVERT: K 87 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8265 (tm-30) REVERT: K 129 ASP cc_start: 0.8832 (t70) cc_final: 0.8623 (t0) REVERT: K 137 GLU cc_start: 0.8555 (tp30) cc_final: 0.8212 (tp30) REVERT: L 44 ASP cc_start: 0.8548 (t0) cc_final: 0.8314 (t0) REVERT: L 70 ARG cc_start: 0.8595 (mmt180) cc_final: 0.7626 (mmm160) REVERT: M 77 LYS cc_start: 0.7121 (tttt) cc_final: 0.6718 (tttt) REVERT: M 112 TYR cc_start: 0.7619 (t80) cc_final: 0.6899 (t80) REVERT: M 254 GLN cc_start: 0.8626 (mp10) cc_final: 0.8319 (mp10) REVERT: O 32 MET cc_start: 0.8302 (tpp) cc_final: 0.8095 (mmm) REVERT: O 261 GLN cc_start: 0.8562 (mp10) cc_final: 0.8249 (mp10) REVERT: O 528 MET cc_start: 0.8172 (pmm) cc_final: 0.7711 (pmm) REVERT: P 225 ILE cc_start: 0.8708 (tp) cc_final: 0.8479 (tp) REVERT: P 251 ASP cc_start: 0.8975 (t0) cc_final: 0.8552 (t0) REVERT: Q 15 TYR cc_start: 0.6561 (t80) cc_final: 0.6103 (t80) REVERT: Q 51 GLU cc_start: 0.8914 (mp0) cc_final: 0.8524 (mp0) REVERT: Q 108 TYR cc_start: 0.6836 (t80) cc_final: 0.6113 (t80) REVERT: Q 112 TYR cc_start: 0.8080 (p90) cc_final: 0.7808 (p90) outliers start: 58 outliers final: 31 residues processed: 493 average time/residue: 0.2616 time to fit residues: 214.1603 Evaluate side-chains 472 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 441 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1217 ILE Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 1035 MET Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 36 CYS Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain N residue 290 ILE Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain P residue 292 SER Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 113 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 443 optimal weight: 6.9990 chunk 30 optimal weight: 0.2980 chunk 391 optimal weight: 1.9990 chunk 486 optimal weight: 6.9990 chunk 465 optimal weight: 2.9990 chunk 479 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 chunk 509 optimal weight: 8.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 600 HIS E 113 GLN ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.072263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.054198 restraints weight = 116844.535| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.63 r_work: 0.2806 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 43025 Z= 0.155 Angle : 0.539 11.652 58330 Z= 0.279 Chirality : 0.042 0.166 6581 Planarity : 0.004 0.049 7312 Dihedral : 10.560 142.516 6340 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.51 % Favored : 96.47 % Rotamer: Outliers : 1.14 % Allowed : 11.79 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.12), residues: 5095 helix: 1.54 (0.12), residues: 1902 sheet: -0.35 (0.19), residues: 744 loop : -0.75 (0.12), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 48 TYR 0.022 0.001 TYR D 50 PHE 0.023 0.001 PHE D 145 TRP 0.017 0.001 TRP A 201 HIS 0.007 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00357 (42997) covalent geometry : angle 0.53254 (58297) hydrogen bonds : bond 0.03696 ( 1692) hydrogen bonds : angle 4.35999 ( 4704) metal coordination : bond 0.00691 ( 27) metal coordination : angle 3.65092 ( 33) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 459 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 736 HIS cc_start: 0.7769 (t-90) cc_final: 0.7463 (t-90) REVERT: A 1117 MET cc_start: 0.7874 (mmm) cc_final: 0.7371 (mmp) REVERT: A 1172 TYR cc_start: 0.8048 (p90) cc_final: 0.7831 (p90) REVERT: B 84 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.6815 (pt) REVERT: B 800 ASN cc_start: 0.8578 (t0) cc_final: 0.8057 (t0) REVERT: C 240 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8221 (mmtm) REVERT: D 13 ASP cc_start: 0.8791 (m-30) cc_final: 0.7399 (m-30) REVERT: D 98 MET cc_start: 0.8083 (ptm) cc_final: 0.7347 (ppp) REVERT: D 107 MET cc_start: 0.9275 (mmm) cc_final: 0.8896 (mmm) REVERT: D 135 TYR cc_start: 0.8473 (m-80) cc_final: 0.7791 (m-80) REVERT: E 113 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7519 (mm-40) REVERT: E 122 LYS cc_start: 0.8458 (pttp) cc_final: 0.7475 (pttp) REVERT: F 110 ASP cc_start: 0.8563 (p0) cc_final: 0.8211 (p0) REVERT: G 114 MET cc_start: 0.8151 (mtm) cc_final: 0.7891 (mtm) REVERT: G 120 TYR cc_start: 0.8076 (p90) cc_final: 0.7867 (p90) REVERT: G 130 TRP cc_start: 0.7284 (t60) cc_final: 0.7044 (t60) REVERT: H 52 GLN cc_start: 0.9445 (mm-40) cc_final: 0.9120 (mm-40) REVERT: H 83 GLN cc_start: 0.8259 (mp10) cc_final: 0.8014 (mp10) REVERT: K 87 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8225 (tm-30) REVERT: K 129 ASP cc_start: 0.8837 (t70) cc_final: 0.8607 (t0) REVERT: K 137 GLU cc_start: 0.8544 (tp30) cc_final: 0.8223 (tp30) REVERT: M 77 LYS cc_start: 0.7130 (tttt) cc_final: 0.6803 (tttt) REVERT: M 227 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7602 (pp) REVERT: M 254 GLN cc_start: 0.8579 (mp10) cc_final: 0.8295 (mp10) REVERT: O 32 MET cc_start: 0.8273 (tpp) cc_final: 0.8051 (mmm) REVERT: O 261 GLN cc_start: 0.8592 (mp10) cc_final: 0.8275 (mp10) REVERT: O 528 MET cc_start: 0.8171 (pmm) cc_final: 0.7730 (pmm) REVERT: P 225 ILE cc_start: 0.8722 (tp) cc_final: 0.8447 (tp) REVERT: P 251 ASP cc_start: 0.8995 (t0) cc_final: 0.8566 (t0) REVERT: Q 15 TYR cc_start: 0.6499 (t80) cc_final: 0.5973 (t80) REVERT: Q 16 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6388 (mmp) REVERT: Q 51 GLU cc_start: 0.8911 (mp0) cc_final: 0.8384 (mp0) REVERT: Q 108 TYR cc_start: 0.6852 (t80) cc_final: 0.6090 (t80) outliers start: 52 outliers final: 33 residues processed: 487 average time/residue: 0.2580 time to fit residues: 209.1764 Evaluate side-chains 472 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 435 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 953 MET Chi-restraints excluded: chain B residue 1035 MET Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 36 CYS Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 292 SER Chi-restraints excluded: chain Q residue 16 MET Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 113 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 260 optimal weight: 2.9990 chunk 386 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 408 optimal weight: 2.9990 chunk 281 optimal weight: 6.9990 chunk 480 optimal weight: 8.9990 chunk 243 optimal weight: 0.5980 chunk 457 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 ASN D 74 ASN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.071423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.053365 restraints weight = 116905.958| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.61 r_work: 0.2783 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 43025 Z= 0.226 Angle : 0.579 13.350 58330 Z= 0.297 Chirality : 0.043 0.172 6581 Planarity : 0.004 0.048 7312 Dihedral : 10.566 143.066 6340 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.98 % Favored : 96.00 % Rotamer: Outliers : 1.69 % Allowed : 12.84 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.12), residues: 5095 helix: 1.54 (0.12), residues: 1903 sheet: -0.39 (0.19), residues: 757 loop : -0.77 (0.12), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 121 TYR 0.021 0.001 TYR D 50 PHE 0.021 0.001 PHE D 145 TRP 0.018 0.002 TRP A 201 HIS 0.011 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00520 (42997) covalent geometry : angle 0.57094 (58297) hydrogen bonds : bond 0.03851 ( 1692) hydrogen bonds : angle 4.38848 ( 4704) metal coordination : bond 0.00930 ( 27) metal coordination : angle 3.98321 ( 33) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 444 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 736 HIS cc_start: 0.7789 (t-90) cc_final: 0.7502 (t-90) REVERT: A 1117 MET cc_start: 0.7852 (mmm) cc_final: 0.7284 (mmp) REVERT: A 1172 TYR cc_start: 0.8068 (p90) cc_final: 0.7851 (p90) REVERT: B 84 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.6834 (pt) REVERT: B 360 MET cc_start: 0.8957 (mtp) cc_final: 0.8714 (mtp) REVERT: B 800 ASN cc_start: 0.8616 (t0) cc_final: 0.8105 (t0) REVERT: B 885 MET cc_start: 0.8640 (tmm) cc_final: 0.8335 (tmm) REVERT: C 240 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8249 (mmtm) REVERT: D 60 ARG cc_start: 0.8954 (tpp-160) cc_final: 0.8278 (tpm170) REVERT: D 98 MET cc_start: 0.8125 (ptm) cc_final: 0.7312 (ppp) REVERT: D 107 MET cc_start: 0.9336 (mmm) cc_final: 0.9132 (mmm) REVERT: D 125 ASN cc_start: 0.8530 (t0) cc_final: 0.8007 (t0) REVERT: D 131 MET cc_start: 0.8538 (ttt) cc_final: 0.7928 (ttm) REVERT: D 135 TYR cc_start: 0.8564 (m-80) cc_final: 0.8109 (m-80) REVERT: E 122 LYS cc_start: 0.8528 (pttp) cc_final: 0.7582 (pttp) REVERT: F 110 ASP cc_start: 0.8612 (p0) cc_final: 0.8338 (p0) REVERT: G 114 MET cc_start: 0.8166 (mtm) cc_final: 0.7924 (mtm) REVERT: G 130 TRP cc_start: 0.7229 (t60) cc_final: 0.7023 (t60) REVERT: H 45 GLU cc_start: 0.9104 (tt0) cc_final: 0.8843 (tm-30) REVERT: H 83 GLN cc_start: 0.8263 (mp10) cc_final: 0.7994 (mp10) REVERT: I 92 GLU cc_start: 0.6372 (mt-10) cc_final: 0.6047 (mp0) REVERT: K 87 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8234 (tm-30) REVERT: K 137 GLU cc_start: 0.8551 (tp30) cc_final: 0.8210 (tp30) REVERT: M 77 LYS cc_start: 0.7169 (tttt) cc_final: 0.6766 (tttt) REVERT: M 112 TYR cc_start: 0.7577 (t80) cc_final: 0.6811 (t80) REVERT: M 227 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7639 (pp) REVERT: M 254 GLN cc_start: 0.8588 (mp10) cc_final: 0.8309 (mp10) REVERT: O 261 GLN cc_start: 0.8605 (mp10) cc_final: 0.8301 (mp10) REVERT: O 528 MET cc_start: 0.8238 (pmm) cc_final: 0.7766 (pmm) REVERT: P 225 ILE cc_start: 0.8758 (tp) cc_final: 0.8474 (tp) REVERT: P 251 ASP cc_start: 0.8982 (t0) cc_final: 0.8546 (t0) REVERT: Q 15 TYR cc_start: 0.6538 (t80) cc_final: 0.6071 (t80) REVERT: Q 16 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6739 (mmp) REVERT: Q 51 GLU cc_start: 0.8897 (mp0) cc_final: 0.8658 (mp0) REVERT: Q 52 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8298 (tpt-90) REVERT: Q 108 TYR cc_start: 0.6856 (t80) cc_final: 0.6136 (t80) outliers start: 77 outliers final: 45 residues processed: 493 average time/residue: 0.2566 time to fit residues: 211.2860 Evaluate side-chains 484 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 435 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1217 ILE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 953 MET Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 36 CYS Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain P residue 292 SER Chi-restraints excluded: chain Q residue 16 MET Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 52 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 356 optimal weight: 0.7980 chunk 320 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 381 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 420 optimal weight: 7.9990 chunk 468 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 461 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 344 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.072039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.053974 restraints weight = 116935.610| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.62 r_work: 0.2800 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 43025 Z= 0.171 Angle : 0.548 11.314 58330 Z= 0.282 Chirality : 0.042 0.171 6581 Planarity : 0.004 0.049 7312 Dihedral : 10.505 143.212 6340 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.49 % Favored : 96.49 % Rotamer: Outliers : 1.62 % Allowed : 13.54 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.12), residues: 5095 helix: 1.63 (0.12), residues: 1903 sheet: -0.35 (0.19), residues: 755 loop : -0.72 (0.12), residues: 2437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 48 TYR 0.022 0.001 TYR Q 112 PHE 0.019 0.001 PHE D 145 TRP 0.017 0.001 TRP A 201 HIS 0.008 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00395 (42997) covalent geometry : angle 0.54176 (58297) hydrogen bonds : bond 0.03603 ( 1692) hydrogen bonds : angle 4.29131 ( 4704) metal coordination : bond 0.00718 ( 27) metal coordination : angle 3.55534 ( 33) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 453 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 736 HIS cc_start: 0.7772 (t-90) cc_final: 0.7495 (t-90) REVERT: A 1117 MET cc_start: 0.7847 (mmm) cc_final: 0.7253 (mmp) REVERT: B 84 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.6940 (pt) REVERT: B 351 MET cc_start: 0.8673 (mmp) cc_final: 0.8329 (mmp) REVERT: B 360 MET cc_start: 0.8954 (mtp) cc_final: 0.8700 (mtp) REVERT: B 800 ASN cc_start: 0.8628 (t0) cc_final: 0.8110 (t0) REVERT: C 240 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8300 (mmtm) REVERT: D 98 MET cc_start: 0.8137 (ptm) cc_final: 0.7542 (ppp) REVERT: D 107 MET cc_start: 0.9363 (mmm) cc_final: 0.9098 (mmm) REVERT: D 125 ASN cc_start: 0.8486 (t0) cc_final: 0.8222 (t0) REVERT: D 131 MET cc_start: 0.8517 (ttt) cc_final: 0.7869 (ttm) REVERT: D 135 TYR cc_start: 0.8511 (m-80) cc_final: 0.8089 (m-80) REVERT: E 114 ASN cc_start: 0.8836 (t0) cc_final: 0.8574 (t0) REVERT: E 122 LYS cc_start: 0.8512 (pttp) cc_final: 0.7576 (pttp) REVERT: F 110 ASP cc_start: 0.8632 (p0) cc_final: 0.8325 (p0) REVERT: F 114 GLU cc_start: 0.8148 (tp30) cc_final: 0.7896 (tp30) REVERT: F 119 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7796 (mtm-85) REVERT: G 114 MET cc_start: 0.8149 (mtm) cc_final: 0.7902 (mtm) REVERT: G 130 TRP cc_start: 0.7214 (t60) cc_final: 0.7005 (t60) REVERT: H 45 GLU cc_start: 0.9097 (tt0) cc_final: 0.8835 (tm-30) REVERT: H 52 GLN cc_start: 0.9373 (mm-40) cc_final: 0.9152 (mm-40) REVERT: H 83 GLN cc_start: 0.8271 (mp10) cc_final: 0.7996 (mp10) REVERT: I 92 GLU cc_start: 0.6369 (mt-10) cc_final: 0.6076 (mp0) REVERT: K 68 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7963 (mm-30) REVERT: K 87 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8212 (tm-30) REVERT: K 137 GLU cc_start: 0.8565 (tp30) cc_final: 0.8230 (tp30) REVERT: M 77 LYS cc_start: 0.7070 (tttt) cc_final: 0.6619 (tttt) REVERT: M 112 TYR cc_start: 0.7627 (t80) cc_final: 0.6844 (t80) REVERT: M 227 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7657 (pp) REVERT: M 254 GLN cc_start: 0.8572 (mp10) cc_final: 0.8296 (mp10) REVERT: O 261 GLN cc_start: 0.8591 (mp10) cc_final: 0.8286 (mp10) REVERT: O 528 MET cc_start: 0.8234 (pmm) cc_final: 0.7725 (pmm) REVERT: P 179 LEU cc_start: 0.8814 (mm) cc_final: 0.8611 (mp) REVERT: P 225 ILE cc_start: 0.8728 (tp) cc_final: 0.8460 (tp) REVERT: P 251 ASP cc_start: 0.8990 (t0) cc_final: 0.8567 (t0) REVERT: Q 15 TYR cc_start: 0.6547 (t80) cc_final: 0.6065 (t80) REVERT: Q 16 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6549 (mmp) REVERT: Q 51 GLU cc_start: 0.8909 (mp0) cc_final: 0.8463 (mp0) REVERT: Q 52 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8204 (tpt-90) REVERT: Q 108 TYR cc_start: 0.6998 (t80) cc_final: 0.6361 (t80) outliers start: 74 outliers final: 50 residues processed: 501 average time/residue: 0.2580 time to fit residues: 215.7609 Evaluate side-chains 494 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 440 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1217 ILE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 953 MET Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 36 CYS Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain P residue 292 SER Chi-restraints excluded: chain Q residue 16 MET Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 52 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 227 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 279 optimal weight: 9.9990 chunk 467 optimal weight: 4.9990 chunk 507 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 329 optimal weight: 9.9990 chunk 311 optimal weight: 2.9990 chunk 361 optimal weight: 10.0000 chunk 433 optimal weight: 5.9990 chunk 332 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 GLN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 GLN P 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.070149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.052029 restraints weight = 118539.482| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.62 r_work: 0.2749 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.109 43025 Z= 0.336 Angle : 0.682 16.100 58330 Z= 0.346 Chirality : 0.046 0.195 6581 Planarity : 0.004 0.055 7312 Dihedral : 10.639 143.742 6340 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.85 % Favored : 95.13 % Rotamer: Outliers : 1.87 % Allowed : 14.33 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.12), residues: 5095 helix: 1.41 (0.12), residues: 1902 sheet: -0.47 (0.19), residues: 750 loop : -0.84 (0.12), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 48 TYR 0.028 0.002 TYR Q 112 PHE 0.022 0.002 PHE A 474 TRP 0.021 0.002 TRP A 201 HIS 0.013 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00773 (42997) covalent geometry : angle 0.67267 (58297) hydrogen bonds : bond 0.04292 ( 1692) hydrogen bonds : angle 4.57620 ( 4704) metal coordination : bond 0.01357 ( 27) metal coordination : angle 4.77779 ( 33) Misc. bond : bond 0.00073 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 449 time to evaluate : 1.771 Fit side-chains revert: symmetry clash REVERT: A 1117 MET cc_start: 0.7984 (mmm) cc_final: 0.7389 (mmp) REVERT: A 1172 TYR cc_start: 0.8134 (p90) cc_final: 0.6697 (p90) REVERT: B 84 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.6642 (pt) REVERT: B 800 ASN cc_start: 0.8666 (t0) cc_final: 0.8151 (t0) REVERT: B 987 MET cc_start: 0.8646 (mmp) cc_final: 0.8399 (mmp) REVERT: C 240 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8265 (mmtm) REVERT: D 60 ARG cc_start: 0.8923 (tpp-160) cc_final: 0.8371 (tpm170) REVERT: D 98 MET cc_start: 0.8178 (ptm) cc_final: 0.7531 (ppp) REVERT: D 107 MET cc_start: 0.9393 (mmm) cc_final: 0.9141 (mmm) REVERT: D 131 MET cc_start: 0.8562 (ttt) cc_final: 0.7870 (ttm) REVERT: D 135 TYR cc_start: 0.8606 (m-80) cc_final: 0.8115 (m-80) REVERT: E 122 LYS cc_start: 0.8587 (pttp) cc_final: 0.7634 (pttp) REVERT: G 114 MET cc_start: 0.8213 (mtm) cc_final: 0.7995 (mtm) REVERT: G 130 TRP cc_start: 0.7255 (t60) cc_final: 0.7011 (t60) REVERT: H 45 GLU cc_start: 0.9132 (tt0) cc_final: 0.8849 (tm-30) REVERT: H 52 GLN cc_start: 0.9414 (mm-40) cc_final: 0.9194 (mm-40) REVERT: H 83 GLN cc_start: 0.8251 (mp10) cc_final: 0.7984 (mp10) REVERT: I 43 ARG cc_start: 0.8669 (ttm170) cc_final: 0.7768 (ttm170) REVERT: K 68 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8078 (mm-30) REVERT: K 87 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8214 (tm-30) REVERT: K 137 GLU cc_start: 0.8576 (tp30) cc_final: 0.8189 (tp30) REVERT: M 77 LYS cc_start: 0.7051 (tttt) cc_final: 0.6819 (tttt) REVERT: M 112 TYR cc_start: 0.7701 (t80) cc_final: 0.7115 (t80) REVERT: M 227 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7703 (pp) REVERT: M 254 GLN cc_start: 0.8606 (mp10) cc_final: 0.8319 (mp10) REVERT: N 394 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8648 (m) REVERT: O 261 GLN cc_start: 0.8619 (mp10) cc_final: 0.8326 (mp10) REVERT: O 528 MET cc_start: 0.8251 (pmm) cc_final: 0.7703 (pmm) REVERT: P 179 LEU cc_start: 0.8835 (mm) cc_final: 0.8627 (mp) REVERT: P 225 ILE cc_start: 0.8821 (tp) cc_final: 0.8543 (tp) REVERT: P 251 ASP cc_start: 0.9003 (t0) cc_final: 0.8548 (t0) REVERT: P 259 ASP cc_start: 0.8077 (t0) cc_final: 0.7856 (t0) REVERT: Q 15 TYR cc_start: 0.6614 (t80) cc_final: 0.6176 (t80) REVERT: Q 16 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6128 (mmt) REVERT: Q 51 GLU cc_start: 0.8915 (mp0) cc_final: 0.8387 (mp0) REVERT: Q 108 TYR cc_start: 0.6892 (t80) cc_final: 0.6332 (t80) outliers start: 85 outliers final: 56 residues processed: 505 average time/residue: 0.2513 time to fit residues: 212.3566 Evaluate side-chains 499 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 439 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1217 ILE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1316 THR Chi-restraints excluded: chain A residue 1379 MET Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 953 MET Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 36 CYS Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain P residue 292 SER Chi-restraints excluded: chain Q residue 16 MET Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 52 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 398 optimal weight: 0.9980 chunk 434 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 337 optimal weight: 0.8980 chunk 315 optimal weight: 0.4980 chunk 433 optimal weight: 6.9990 chunk 201 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 chunk 459 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 GLN P 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.072733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.054702 restraints weight = 116426.785| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.62 r_work: 0.2821 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 43025 Z= 0.118 Angle : 0.541 10.136 58330 Z= 0.279 Chirality : 0.042 0.171 6581 Planarity : 0.004 0.050 7312 Dihedral : 10.460 143.365 6340 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.12 % Favored : 96.86 % Rotamer: Outliers : 1.38 % Allowed : 15.12 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.12), residues: 5095 helix: 1.68 (0.12), residues: 1901 sheet: -0.38 (0.19), residues: 748 loop : -0.70 (0.13), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 48 TYR 0.030 0.001 TYR Q 112 PHE 0.019 0.001 PHE D 145 TRP 0.014 0.001 TRP O 215 HIS 0.011 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00267 (42997) covalent geometry : angle 0.53584 (58297) hydrogen bonds : bond 0.03408 ( 1692) hydrogen bonds : angle 4.25567 ( 4704) metal coordination : bond 0.00486 ( 27) metal coordination : angle 3.03208 ( 33) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 468 time to evaluate : 2.257 Fit side-chains revert: symmetry clash REVERT: A 736 HIS cc_start: 0.7677 (t-90) cc_final: 0.7376 (t-90) REVERT: A 1104 MET cc_start: 0.7877 (tmm) cc_final: 0.7149 (ptt) REVERT: A 1117 MET cc_start: 0.7795 (mmm) cc_final: 0.7188 (mmp) REVERT: A 1172 TYR cc_start: 0.8040 (p90) cc_final: 0.6353 (p90) REVERT: B 84 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7001 (pt) REVERT: B 155 MET cc_start: 0.9022 (ttm) cc_final: 0.8734 (ttp) REVERT: B 351 MET cc_start: 0.8653 (mmp) cc_final: 0.8318 (mmp) REVERT: B 360 MET cc_start: 0.8973 (mtp) cc_final: 0.8751 (mtp) REVERT: B 800 ASN cc_start: 0.8558 (t0) cc_final: 0.8026 (t0) REVERT: B 987 MET cc_start: 0.8605 (mmp) cc_final: 0.8331 (mmp) REVERT: C 240 LYS cc_start: 0.8560 (mmtt) cc_final: 0.8256 (mmtm) REVERT: C 287 ASP cc_start: 0.8868 (m-30) cc_final: 0.8428 (t0) REVERT: D 98 MET cc_start: 0.8229 (ptm) cc_final: 0.7623 (ppp) REVERT: D 107 MET cc_start: 0.9370 (mmm) cc_final: 0.9108 (mmm) REVERT: D 131 MET cc_start: 0.8464 (ttt) cc_final: 0.7791 (ttm) REVERT: D 135 TYR cc_start: 0.8608 (m-80) cc_final: 0.8370 (m-80) REVERT: D 145 PHE cc_start: 0.7550 (m-80) cc_final: 0.6905 (t80) REVERT: E 122 LYS cc_start: 0.8497 (pttp) cc_final: 0.7558 (pttp) REVERT: E 215 MET cc_start: 0.8083 (tpp) cc_final: 0.7815 (tpp) REVERT: F 114 GLU cc_start: 0.8097 (tp30) cc_final: 0.7849 (tp30) REVERT: F 119 ARG cc_start: 0.8069 (mtm-85) cc_final: 0.7777 (mtm-85) REVERT: G 114 MET cc_start: 0.8160 (mtm) cc_final: 0.7922 (mtm) REVERT: H 45 GLU cc_start: 0.9078 (tt0) cc_final: 0.8827 (tm-30) REVERT: H 52 GLN cc_start: 0.9428 (mm-40) cc_final: 0.9223 (mm-40) REVERT: H 83 GLN cc_start: 0.8258 (mp10) cc_final: 0.7992 (mp10) REVERT: I 43 ARG cc_start: 0.8540 (ttm170) cc_final: 0.7510 (ttm170) REVERT: K 68 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7997 (mm-30) REVERT: K 87 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8209 (tm-30) REVERT: K 137 GLU cc_start: 0.8578 (tp30) cc_final: 0.8267 (tp30) REVERT: M 77 LYS cc_start: 0.6992 (tttt) cc_final: 0.6727 (tttt) REVERT: M 112 TYR cc_start: 0.7601 (t80) cc_final: 0.6823 (t80) REVERT: M 227 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7697 (pp) REVERT: M 254 GLN cc_start: 0.8543 (mp10) cc_final: 0.8265 (mp10) REVERT: O 261 GLN cc_start: 0.8569 (mp10) cc_final: 0.8261 (mp10) REVERT: O 528 MET cc_start: 0.8201 (pmm) cc_final: 0.7627 (pmm) REVERT: P 225 ILE cc_start: 0.8724 (tp) cc_final: 0.8387 (tp) REVERT: P 229 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7432 (tm-30) REVERT: P 251 ASP cc_start: 0.8999 (t0) cc_final: 0.8596 (t0) REVERT: Q 15 TYR cc_start: 0.6549 (t80) cc_final: 0.6064 (t80) REVERT: Q 16 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6548 (mmp) REVERT: Q 51 GLU cc_start: 0.8892 (mp0) cc_final: 0.8415 (mp0) REVERT: Q 52 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8218 (tpt-90) REVERT: Q 108 TYR cc_start: 0.6891 (t80) cc_final: 0.6319 (t80) outliers start: 63 outliers final: 38 residues processed: 504 average time/residue: 0.2617 time to fit residues: 219.4690 Evaluate side-chains 487 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 445 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1217 ILE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1393 THR Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 1035 MET Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 36 CYS Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 16 MET Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain Q residue 65 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 299 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 505 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 471 optimal weight: 0.9990 chunk 255 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 153 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN B 39 ASN E 113 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.072755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.054714 restraints weight = 116219.439| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.62 r_work: 0.2823 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 43025 Z= 0.130 Angle : 0.542 10.461 58330 Z= 0.278 Chirality : 0.042 0.175 6581 Planarity : 0.004 0.048 7312 Dihedral : 10.404 143.741 6340 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.45 % Rotamer: Outliers : 1.32 % Allowed : 15.58 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.12), residues: 5095 helix: 1.73 (0.12), residues: 1910 sheet: -0.32 (0.19), residues: 751 loop : -0.64 (0.13), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 48 TYR 0.032 0.001 TYR P 261 PHE 0.017 0.001 PHE D 145 TRP 0.017 0.001 TRP A 201 HIS 0.011 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00300 (42997) covalent geometry : angle 0.53750 (58297) hydrogen bonds : bond 0.03360 ( 1692) hydrogen bonds : angle 4.20050 ( 4704) metal coordination : bond 0.00502 ( 27) metal coordination : angle 2.96427 ( 33) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 447 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1117 MET cc_start: 0.7796 (mmm) cc_final: 0.7165 (mmp) REVERT: B 84 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.6987 (pt) REVERT: B 155 MET cc_start: 0.9006 (ttm) cc_final: 0.8742 (ttp) REVERT: B 215 ILE cc_start: 0.8267 (mp) cc_final: 0.7988 (mp) REVERT: B 351 MET cc_start: 0.8656 (mmp) cc_final: 0.8325 (mmp) REVERT: B 800 ASN cc_start: 0.8557 (t0) cc_final: 0.8016 (t0) REVERT: B 987 MET cc_start: 0.8645 (mmp) cc_final: 0.8381 (mmp) REVERT: C 240 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8215 (mmtm) REVERT: D 60 ARG cc_start: 0.8853 (tpp-160) cc_final: 0.8353 (tpm170) REVERT: D 98 MET cc_start: 0.8311 (ptm) cc_final: 0.7610 (ppp) REVERT: D 107 MET cc_start: 0.9378 (mmm) cc_final: 0.9098 (mmm) REVERT: D 131 MET cc_start: 0.8502 (ttt) cc_final: 0.7791 (ttm) REVERT: D 135 TYR cc_start: 0.8554 (m-80) cc_final: 0.8312 (m-80) REVERT: D 145 PHE cc_start: 0.7569 (m-80) cc_final: 0.7039 (t80) REVERT: F 114 GLU cc_start: 0.8109 (tp30) cc_final: 0.7328 (mm-30) REVERT: G 114 MET cc_start: 0.8147 (mtm) cc_final: 0.7905 (mtm) REVERT: H 45 GLU cc_start: 0.9124 (tt0) cc_final: 0.8797 (tm-30) REVERT: H 52 GLN cc_start: 0.9438 (mm-40) cc_final: 0.9234 (mm-40) REVERT: H 83 GLN cc_start: 0.8263 (mp10) cc_final: 0.8001 (mp10) REVERT: K 68 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7988 (mm-30) REVERT: K 87 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8234 (tm-30) REVERT: K 137 GLU cc_start: 0.8529 (tp30) cc_final: 0.8308 (tp30) REVERT: M 77 LYS cc_start: 0.6975 (tttt) cc_final: 0.6690 (tttt) REVERT: M 112 TYR cc_start: 0.7597 (t80) cc_final: 0.6844 (t80) REVERT: M 227 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7688 (pp) REVERT: M 254 GLN cc_start: 0.8550 (mp10) cc_final: 0.8275 (mp10) REVERT: O 261 GLN cc_start: 0.8552 (mp10) cc_final: 0.8248 (mp10) REVERT: O 528 MET cc_start: 0.8093 (pmm) cc_final: 0.7509 (pmm) REVERT: P 164 TRP cc_start: 0.8282 (OUTLIER) cc_final: 0.7161 (m100) REVERT: P 225 ILE cc_start: 0.8740 (tp) cc_final: 0.8375 (tp) REVERT: P 229 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7196 (tm-30) REVERT: P 251 ASP cc_start: 0.9002 (t0) cc_final: 0.8652 (t0) REVERT: Q 15 TYR cc_start: 0.6576 (t80) cc_final: 0.6080 (t80) REVERT: Q 16 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6621 (mmp) REVERT: Q 51 GLU cc_start: 0.8891 (mp0) cc_final: 0.8382 (mp0) REVERT: Q 108 TYR cc_start: 0.6866 (t80) cc_final: 0.6280 (t80) outliers start: 60 outliers final: 43 residues processed: 484 average time/residue: 0.2579 time to fit residues: 207.7075 Evaluate side-chains 487 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 440 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1217 ILE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 1035 MET Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 36 CYS Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain P residue 164 TRP Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 16 MET Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 325 optimal weight: 3.9990 chunk 237 optimal weight: 5.9990 chunk 420 optimal weight: 0.9980 chunk 321 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 385 optimal weight: 4.9990 chunk 434 optimal weight: 7.9990 chunk 336 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 113 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.071778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.053612 restraints weight = 117013.540| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.62 r_work: 0.2794 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 43025 Z= 0.203 Angle : 0.586 12.233 58330 Z= 0.299 Chirality : 0.043 0.184 6581 Planarity : 0.004 0.046 7312 Dihedral : 10.435 144.217 6340 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.93 % Favored : 96.05 % Rotamer: Outliers : 1.25 % Allowed : 15.63 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.12), residues: 5095 helix: 1.68 (0.12), residues: 1905 sheet: -0.33 (0.19), residues: 752 loop : -0.68 (0.13), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 48 TYR 0.028 0.001 TYR Q 112 PHE 0.018 0.001 PHE A 474 TRP 0.018 0.002 TRP A 201 HIS 0.012 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00468 (42997) covalent geometry : angle 0.57946 (58297) hydrogen bonds : bond 0.03621 ( 1692) hydrogen bonds : angle 4.28404 ( 4704) metal coordination : bond 0.00808 ( 27) metal coordination : angle 3.59798 ( 33) Misc. bond : bond 0.00041 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 439 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 760 GLN cc_start: 0.8977 (mt0) cc_final: 0.8671 (mt0) REVERT: A 1117 MET cc_start: 0.7868 (mmm) cc_final: 0.7221 (mmp) REVERT: B 84 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7038 (pt) REVERT: B 123 MET cc_start: 0.8796 (mtt) cc_final: 0.8494 (mtt) REVERT: B 155 MET cc_start: 0.9005 (ttm) cc_final: 0.8689 (ttp) REVERT: B 351 MET cc_start: 0.8675 (mmp) cc_final: 0.8324 (mmp) REVERT: B 800 ASN cc_start: 0.8573 (t0) cc_final: 0.8034 (t0) REVERT: B 987 MET cc_start: 0.8653 (mmp) cc_final: 0.8398 (mmp) REVERT: C 240 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8206 (mmtm) REVERT: D 60 ARG cc_start: 0.8904 (tpp-160) cc_final: 0.8390 (tpm170) REVERT: D 98 MET cc_start: 0.8215 (ptm) cc_final: 0.7619 (ppp) REVERT: D 107 MET cc_start: 0.9379 (mmm) cc_final: 0.9091 (mmm) REVERT: D 131 MET cc_start: 0.8525 (ttt) cc_final: 0.7787 (ttm) REVERT: D 135 TYR cc_start: 0.8579 (m-80) cc_final: 0.8257 (m-80) REVERT: F 114 GLU cc_start: 0.8312 (tp30) cc_final: 0.8083 (tp30) REVERT: G 112 GLN cc_start: 0.8308 (tp40) cc_final: 0.8102 (mm-40) REVERT: G 114 MET cc_start: 0.8175 (mtm) cc_final: 0.7947 (mtm) REVERT: H 45 GLU cc_start: 0.9126 (tt0) cc_final: 0.8842 (tm-30) REVERT: H 52 GLN cc_start: 0.9450 (mm-40) cc_final: 0.9250 (mm-40) REVERT: H 83 GLN cc_start: 0.8304 (mp10) cc_final: 0.8022 (mp10) REVERT: K 68 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8026 (mm-30) REVERT: K 87 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8201 (tm-30) REVERT: K 137 GLU cc_start: 0.8596 (tp30) cc_final: 0.8369 (tp30) REVERT: M 77 LYS cc_start: 0.7042 (tttt) cc_final: 0.6747 (tttt) REVERT: M 112 TYR cc_start: 0.7642 (t80) cc_final: 0.7026 (t80) REVERT: M 227 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7687 (pp) REVERT: M 254 GLN cc_start: 0.8559 (mp10) cc_final: 0.8287 (mp10) REVERT: N 394 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8613 (m) REVERT: O 261 GLN cc_start: 0.8579 (mp10) cc_final: 0.8277 (mp10) REVERT: O 528 MET cc_start: 0.8146 (pmm) cc_final: 0.7613 (pmm) REVERT: O 629 MET cc_start: 0.8250 (mpp) cc_final: 0.8026 (mpp) REVERT: P 164 TRP cc_start: 0.8362 (OUTLIER) cc_final: 0.7260 (m100) REVERT: P 225 ILE cc_start: 0.8749 (tp) cc_final: 0.8455 (tp) REVERT: P 251 ASP cc_start: 0.9004 (t0) cc_final: 0.8608 (t0) REVERT: Q 15 TYR cc_start: 0.6596 (t80) cc_final: 0.6136 (t80) REVERT: Q 16 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6863 (mmp) REVERT: Q 51 GLU cc_start: 0.8910 (mp0) cc_final: 0.8336 (mp0) REVERT: Q 52 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8358 (tpt-90) REVERT: Q 108 TYR cc_start: 0.6979 (t80) cc_final: 0.6401 (t80) outliers start: 57 outliers final: 43 residues processed: 476 average time/residue: 0.2586 time to fit residues: 205.9645 Evaluate side-chains 484 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 435 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1217 ILE Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 1035 MET Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 36 CYS Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain P residue 164 TRP Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 16 MET Chi-restraints excluded: chain Q residue 52 ARG Chi-restraints excluded: chain Q residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 37 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 477 optimal weight: 3.9990 chunk 407 optimal weight: 7.9990 chunk 486 optimal weight: 3.9990 chunk 316 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 366 optimal weight: 10.0000 chunk 461 optimal weight: 6.9990 chunk 490 optimal weight: 9.9990 chunk 395 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.071951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.053860 restraints weight = 117537.032| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.63 r_work: 0.2798 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 43025 Z= 0.183 Angle : 0.574 11.946 58330 Z= 0.294 Chirality : 0.043 0.181 6581 Planarity : 0.004 0.047 7312 Dihedral : 10.417 144.189 6340 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.77 % Favored : 96.21 % Rotamer: Outliers : 1.34 % Allowed : 15.69 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.12), residues: 5095 helix: 1.69 (0.12), residues: 1902 sheet: -0.31 (0.19), residues: 752 loop : -0.68 (0.13), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 48 TYR 0.029 0.001 TYR Q 112 PHE 0.024 0.001 PHE A 474 TRP 0.017 0.002 TRP A 201 HIS 0.012 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00425 (42997) covalent geometry : angle 0.56837 (58297) hydrogen bonds : bond 0.03561 ( 1692) hydrogen bonds : angle 4.26620 ( 4704) metal coordination : bond 0.00724 ( 27) metal coordination : angle 3.55730 ( 33) Misc. bond : bond 0.00032 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9241.70 seconds wall clock time: 160 minutes 2.54 seconds (9602.54 seconds total)