Starting phenix.real_space_refine on Mon Jul 6 05:29:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ol0_12974/07_2026/7ol0_12974.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ol0_12974/07_2026/7ol0_12974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ol0_12974/07_2026/7ol0_12974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ol0_12974/07_2026/7ol0_12974.map" model { file = "/net/cci-nas-00/data/ceres_data/7ol0_12974/07_2026/7ol0_12974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ol0_12974/07_2026/7ol0_12974.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ol0_12974/07_2026/7ol0_12974.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ol0_12974/07_2026/7ol0_12974.cif" } resolution = 3.0 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= 0.005 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 8 6.06 5 P 79 5.49 5 Mg 1 5.21 5 S 197 5.16 5 C 20509 2.51 5 N 5776 2.21 5 O 6322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32892 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1407, 11149 Classifications: {'peptide': 1407} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1338} Chain breaks: 6 Chain: "B" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 9047 Classifications: {'peptide': 1131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1077} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2068 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 967 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 1 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 626 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1347 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 926 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "Z" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 393 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "P" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 279 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 9} Chain: "N" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 549 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "T" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 472 SG CYS A 71 106.569 77.670 76.639 1.00 53.88 S ATOM 494 SG CYS A 74 105.007 80.870 78.101 1.00 51.65 S ATOM 541 SG CYS A 81 102.887 77.697 77.856 1.00 47.27 S ATOM 776 SG CYS A 111 87.497 84.600 33.386 1.00 72.60 S ATOM 804 SG CYS A 114 89.614 87.543 33.425 1.00 75.57 S ATOM 1117 SG CYS A 154 85.969 87.611 31.767 1.00 81.24 S ATOM 1144 SG CYS A 184 88.997 85.785 30.150 1.00 78.86 S ATOM 19765 SG CYS B1196 99.763 93.113 68.722 1.00 50.70 S ATOM 19787 SG CYS B1199 98.218 90.188 66.804 1.00 49.13 S ATOM 19902 SG CYS B1214 101.687 89.862 67.987 1.00 64.85 S ATOM 19923 SG CYS B1217 100.822 92.263 65.112 1.00 65.67 S ATOM 20890 SG CYS C 88 83.056 56.214 137.822 1.00 45.58 S ATOM 20903 SG CYS C 90 85.671 54.722 135.250 1.00 49.65 S ATOM 20934 SG CYS C 94 84.329 52.979 138.255 1.00 35.53 S ATOM 20956 SG CYS C 97 82.103 53.550 135.143 1.00 32.77 S ATOM 28719 SG CYS I 86 18.992 29.905 56.976 1.00 54.12 S ATOM 28743 SG CYS I 89 18.821 26.069 57.828 1.00 57.57 S ATOM 28947 SG CYS I 114 21.598 28.235 59.174 1.00 40.67 S ATOM 28982 SG CYS I 119 21.427 27.291 55.551 1.00 54.61 S ATOM 28173 SG CYS I 17 45.657 34.797 22.009 1.00 57.52 S ATOM 28197 SG CYS I 20 49.210 35.613 23.360 1.00 61.55 S ATOM 28348 SG CYS I 39 47.496 38.102 21.496 1.00 55.85 S ATOM 28367 SG CYS I 42 48.905 34.886 19.818 1.00 67.40 S ATOM 29092 SG CYS J 7 56.902 45.435 118.650 1.00 30.76 S ATOM 29116 SG CYS J 10 55.978 46.550 122.230 1.00 19.20 S ATOM 29380 SG CYS J 44 53.364 46.560 119.338 1.00 22.24 S ATOM 29386 SG CYS J 45 54.599 43.539 121.119 1.00 20.46 S ATOM 30523 SG CYS L 19 92.292 26.372 100.431 1.00 40.79 S ATOM 30542 SG CYS L 22 92.630 23.458 102.811 1.00 46.36 S ATOM 30659 SG CYS L 36 95.613 24.716 101.128 1.00 49.32 S ATOM 30685 SG CYS L 39 92.720 22.921 99.081 1.00 51.95 S Time building chain proxies: 5.81, per 1000 atoms: 0.18 Number of scatterers: 32892 At special positions: 0 Unit cell: (159.6, 149.1, 161.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 197 16.00 P 79 15.00 Mg 1 11.99 O 6322 8.00 N 5776 7.00 C 20509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 81 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 154 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1199 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1214 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1196 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1217 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 42 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 45 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7358 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 49 sheets defined 37.8% alpha, 19.7% beta 29 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.700A pdb=" N GLY A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.569A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 539 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.662A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 removed outlier: 3.593A pdb=" N SER A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.880A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 847 " --> pdb=" O GLY A 843 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY A 858 " --> pdb=" O THR A 854 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 removed outlier: 4.174A pdb=" N ARG A 932 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1018 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1052 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1119 through 1129 removed outlier: 3.700A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1148 removed outlier: 3.628A pdb=" N SER A1147 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1180 through 1184 removed outlier: 3.645A pdb=" N THR A1184 " --> pdb=" O PRO A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1197 Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1294 removed outlier: 3.761A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 4.475A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.825A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 4.027A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1478 through 1483 removed outlier: 3.697A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A1482 " --> pdb=" O LYS A1479 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A1483 " --> pdb=" O CYS A1480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1478 through 1483' Processing helix chain 'B' and resid 98 through 115 removed outlier: 3.887A pdb=" N TRP B 104 " --> pdb=" O GLN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 371 through 385 removed outlier: 3.899A pdb=" N MET B 375 " --> pdb=" O ASP B 371 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 378 " --> pdb=" O MET B 374 " (cutoff:3.500A) Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 408 through 423 Processing helix chain 'B' and resid 434 through 454 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 472 through 502 removed outlier: 3.734A pdb=" N GLY B 483 " --> pdb=" O PHE B 479 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG B 502 " --> pdb=" O LYS B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 512 Processing helix chain 'B' and resid 514 through 528 removed outlier: 3.582A pdb=" N SER B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.788A pdb=" N ALA B 536 " --> pdb=" O GLN B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 559 Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 615 through 624 Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.895A pdb=" N ALA B 639 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 671 Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'B' and resid 722 through 727 Processing helix chain 'B' and resid 729 through 735 Processing helix chain 'B' and resid 744 through 748 Processing helix chain 'B' and resid 755 through 760 Processing helix chain 'B' and resid 776 through 781 removed outlier: 3.636A pdb=" N ILE B 780 " --> pdb=" O PRO B 777 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 781 " --> pdb=" O SER B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 794 Processing helix chain 'B' and resid 795 through 806 removed outlier: 3.514A pdb=" N ASN B 799 " --> pdb=" O GLN B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 843 removed outlier: 3.652A pdb=" N GLU B 842 " --> pdb=" O ARG B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 880 Processing helix chain 'B' and resid 1046 through 1049 Processing helix chain 'B' and resid 1054 through 1071 removed outlier: 3.916A pdb=" N LEU B1058 " --> pdb=" O THR B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1094 Processing helix chain 'B' and resid 1154 through 1158 removed outlier: 3.580A pdb=" N ARG B1157 " --> pdb=" O GLY B1154 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP B1158 " --> pdb=" O ARG B1155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1154 through 1158' Processing helix chain 'B' and resid 1164 through 1175 Processing helix chain 'B' and resid 1176 through 1185 Processing helix chain 'B' and resid 1230 through 1241 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.522A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.565A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.550A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 269 Processing helix chain 'D' and resid 65 through 69 removed outlier: 3.651A pdb=" N GLU D 69 " --> pdb=" O LYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 Processing helix chain 'D' and resid 100 through 112 removed outlier: 3.645A pdb=" N TYR D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 129 Processing helix chain 'D' and resid 135 through 140 removed outlier: 4.010A pdb=" N ALA D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 157 removed outlier: 3.616A pdb=" N ILE D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 180 removed outlier: 3.967A pdb=" N GLN D 170 " --> pdb=" O ASP D 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 24 removed outlier: 3.684A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG E 9 " --> pdb=" O GLU E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 34 removed outlier: 3.514A pdb=" N VAL G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 114 through 118 removed outlier: 3.950A pdb=" N GLU G 118 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.863A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN I 74 " --> pdb=" O ASP I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 107 removed outlier: 4.017A pdb=" N GLU I 105 " --> pdb=" O ALA I 102 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA I 107 " --> pdb=" O ALA I 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.779A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.706A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.962A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 95 removed outlier: 6.781A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.213A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 265 Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.706A pdb=" N LEU B1161 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1137 through 1139 removed outlier: 3.551A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.739A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.829A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB2, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.128A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.715A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB5, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB6, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB7, first strand: chain 'A' and resid 1308 through 1310 removed outlier: 3.723A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1164 through 1165 Processing sheet with id=AB9, first strand: chain 'A' and resid 1243 through 1244 Processing sheet with id=AC1, first strand: chain 'A' and resid 1243 through 1244 removed outlier: 4.722A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC3, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.120A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR G 72 " --> pdb=" O LEU G 7 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.120A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR G 50 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 142 through 143 removed outlier: 3.522A pdb=" N LYS B 164 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP B 204 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR B 202 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU B 170 " --> pdb=" O PRO B 200 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B 227 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 203 " --> pdb=" O PHE B 225 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE B 225 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ILE B 205 " --> pdb=" O LYS B 223 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS B 223 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LYS B 207 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N HIS B 221 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL B 209 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N THR B 219 " --> pdb=" O VAL B 209 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 174 through 176 Processing sheet with id=AC7, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=AC8, first strand: chain 'B' and resid 468 through 471 Processing sheet with id=AC9, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.683A pdb=" N TYR B 294 " --> pdb=" O MET B 316 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AD2, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AD3, first strand: chain 'B' and resid 628 through 629 removed outlier: 5.407A pdb=" N TRP B 650 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 646 " --> pdb=" O TRP B 650 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B 652 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS B 643 " --> pdb=" O ILE B 689 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE B 691 " --> pdb=" O LYS B 643 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N PHE B 645 " --> pdb=" O ILE B 691 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 824 through 828 removed outlier: 4.141A pdb=" N LYS B 994 " --> pdb=" O GLU B 895 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG B1001 " --> pdb=" O VAL B 981 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL B 981 " --> pdb=" O ARG B1001 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL B1003 " --> pdb=" O GLY B 979 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N GLY B 979 " --> pdb=" O VAL B1003 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 824 through 828 removed outlier: 4.141A pdb=" N LYS B 994 " --> pdb=" O GLU B 895 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG B1001 " --> pdb=" O VAL B 981 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL B 981 " --> pdb=" O ARG B1001 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL B1003 " --> pdb=" O GLY B 979 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N GLY B 979 " --> pdb=" O VAL B1003 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL B 984 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 836 through 837 Processing sheet with id=AD7, first strand: chain 'B' and resid 1102 through 1103 removed outlier: 7.110A pdb=" N VAL B 871 " --> pdb=" O GLY B1023 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLN B1025 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET B 873 " --> pdb=" O GLN B1025 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ILE B1042 " --> pdb=" O ASN B 854 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE B 856 " --> pdb=" O ILE B1042 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE B1044 " --> pdb=" O ILE B 856 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 858 " --> pdb=" O ILE B1044 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE B1119 " --> pdb=" O ILE B 859 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 904 through 906 Processing sheet with id=AD9, first strand: chain 'B' and resid 942 through 944 removed outlier: 6.971A pdb=" N THR B 971 " --> pdb=" O ILE B 943 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1190 through 1196 Processing sheet with id=AE2, first strand: chain 'B' and resid 1204 through 1206 Processing sheet with id=AE3, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.673A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.606A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.285A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 60 through 63 removed outlier: 3.859A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE8, first strand: chain 'E' and resid 147 through 150 removed outlier: 6.271A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 84 through 89 removed outlier: 4.171A pdb=" N VAL G 88 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE G 160 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AF2, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 22 Processing sheet with id=AF4, first strand: chain 'Z' and resid 742 through 746 removed outlier: 6.688A pdb=" N THR Z 731 " --> pdb=" O ALA Z 727 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA Z 727 " --> pdb=" O THR Z 731 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG Z 733 " --> pdb=" O LYS Z 725 " (cutoff:3.500A) 1353 hydrogen bonds defined for protein. 3762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 8.42 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6083 1.32 - 1.44: 8339 1.44 - 1.57: 18779 1.57 - 1.69: 154 1.69 - 1.82: 311 Bond restraints: 33666 Sorted by residual: bond pdb=" C GLN A 539 " pdb=" O GLN A 539 " ideal model delta sigma weight residual 1.242 1.198 0.044 1.00e-02 1.00e+04 1.92e+01 bond pdb=" C1' DC N 35 " pdb=" N1 DC N 35 " ideal model delta sigma weight residual 1.468 1.524 -0.056 1.40e-02 5.10e+03 1.59e+01 bond pdb=" C3' DG T 26 " pdb=" O3' DG T 26 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.38e+01 bond pdb=" C1' DT T 27 " pdb=" N1 DT T 27 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.26e+01 bond pdb=" C3' DT T 32 " pdb=" O3' DT T 32 " ideal model delta sigma weight residual 1.435 1.480 -0.045 1.30e-02 5.92e+03 1.20e+01 ... (remaining 33661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 45214 3.11 - 6.21: 551 6.21 - 9.32: 45 9.32 - 12.42: 2 12.42 - 15.53: 1 Bond angle restraints: 45813 Sorted by residual: angle pdb=" N ILE B 673 " pdb=" CA ILE B 673 " pdb=" C ILE B 673 " ideal model delta sigma weight residual 112.96 107.92 5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" N GLU A 961 " pdb=" CA GLU A 961 " pdb=" CB GLU A 961 " ideal model delta sigma weight residual 110.28 117.77 -7.49 1.55e+00 4.16e-01 2.34e+01 angle pdb=" O4' DA T 25 " pdb=" C4' DA T 25 " pdb=" C3' DA T 25 " ideal model delta sigma weight residual 106.00 103.14 2.86 6.00e-01 2.78e+00 2.27e+01 angle pdb=" O4' DC T 24 " pdb=" C4' DC T 24 " pdb=" C3' DC T 24 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.24e+01 angle pdb=" N VAL G 148 " pdb=" CA VAL G 148 " pdb=" C VAL G 148 " ideal model delta sigma weight residual 113.71 109.35 4.36 9.50e-01 1.11e+00 2.11e+01 ... (remaining 45808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 19821 35.42 - 70.83: 569 70.83 - 106.25: 42 106.25 - 141.67: 0 141.67 - 177.09: 1 Dihedral angle restraints: 20433 sinusoidal: 9057 harmonic: 11376 Sorted by residual: dihedral pdb=" CA GLN B 331 " pdb=" C GLN B 331 " pdb=" N ARG B 332 " pdb=" CA ARG B 332 " ideal model delta harmonic sigma weight residual -180.00 -152.74 -27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA ASN G 124 " pdb=" C ASN G 124 " pdb=" N PRO G 125 " pdb=" CA PRO G 125 " ideal model delta harmonic sigma weight residual 180.00 153.22 26.78 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA THR A 686 " pdb=" C THR A 686 " pdb=" N ILE A 687 " pdb=" CA ILE A 687 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 20430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 4803 0.108 - 0.216: 317 0.216 - 0.325: 8 0.325 - 0.433: 4 0.433 - 0.541: 1 Chirality restraints: 5133 Sorted by residual: chirality pdb=" CB ILE A 621 " pdb=" CA ILE A 621 " pdb=" CG1 ILE A 621 " pdb=" CG2 ILE A 621 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.54 2.00e-01 2.50e+01 7.32e+00 chirality pdb=" CB VAL I 72 " pdb=" CA VAL I 72 " pdb=" CG1 VAL I 72 " pdb=" CG2 VAL I 72 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CB ILE A 399 " pdb=" CA ILE A 399 " pdb=" CG1 ILE A 399 " pdb=" CG2 ILE A 399 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 5130 not shown) Planarity restraints: 5659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B1125 " -0.034 2.00e-02 2.50e+03 3.02e-02 1.82e+01 pdb=" CG TYR B1125 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR B1125 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B1125 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR B1125 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B1125 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B1125 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B1125 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 63 " 0.017 2.00e-02 2.50e+03 2.26e-02 8.95e+00 pdb=" CG PHE C 63 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE C 63 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE C 63 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE C 63 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE C 63 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 63 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 64 " -0.049 5.00e-02 4.00e+02 7.48e-02 8.94e+00 pdb=" N PRO D 65 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 65 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 65 " -0.041 5.00e-02 4.00e+02 ... (remaining 5656 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 427 2.64 - 3.20: 28223 3.20 - 3.77: 53684 3.77 - 4.33: 77413 4.33 - 4.90: 124304 Nonbonded interactions: 284051 Sorted by model distance: nonbonded pdb=" O PHE A1247 " pdb=" OD1 ASN A1248 " model vdw 2.073 3.040 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2001 " model vdw 2.112 2.170 nonbonded pdb=" O3' A P 46 " pdb="MG MG A2001 " model vdw 2.129 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2001 " model vdw 2.130 2.170 nonbonded pdb=" O MET A 535 " pdb=" OH TYR A 669 " model vdw 2.204 3.040 ... (remaining 284046 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 33.130 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 : 0.010 0.101 33698 Z= 0.425 Angle : 0.900 15.529 45858 Z= 0.514 Chirality : 0.059 0.541 5133 Planarity : 0.006 0.075 5659 Dihedral : 15.794 177.086 13075 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.06 % Allowed : 0.49 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.12), residues: 3864 helix: -1.09 (0.13), residues: 1341 sheet: -0.72 (0.20), residues: 643 loop : -0.80 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 685 TYR 0.073 0.003 TYR B1125 PHE 0.050 0.003 PHE C 63 TRP 0.021 0.003 TRP B 99 HIS 0.028 0.002 HIS I 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00963 / 0.43 (33666) covalent geometry : angle 0.88849 / 0.51 (45813) hydrogen bonds : bond 0.18538 / 12.37 ( 1386) hydrogen bonds : angle 7.59885 / 5.38 ( 3902) metal coordination : bond 0.01171 / 0.84 ( 32) metal coordination : angle 4.64343 / 3.36 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 523 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 514 GLU cc_start: 0.8156 (pt0) cc_final: 0.7706 (pt0) REVERT: A 735 GLN cc_start: 0.7614 (mp10) cc_final: 0.7216 (mp-120) REVERT: A 950 ASN cc_start: 0.8261 (m110) cc_final: 0.8002 (m-40) REVERT: A 1236 ASN cc_start: 0.6823 (m-40) cc_final: 0.6552 (m-40) REVERT: B 206 THR cc_start: 0.8330 (p) cc_final: 0.8073 (p) REVERT: B 685 ARG cc_start: 0.8187 (ttt-90) cc_final: 0.7934 (ttt-90) REVERT: B 761 GLU cc_start: 0.7525 (tp30) cc_final: 0.7312 (mm-30) REVERT: B 915 GLN cc_start: 0.7537 (tt0) cc_final: 0.7317 (tt0) REVERT: B 1169 ASP cc_start: 0.7739 (m-30) cc_final: 0.7332 (m-30) REVERT: E 70 ASP cc_start: 0.6239 (m-30) cc_final: 0.6026 (m-30) REVERT: E 116 GLN cc_start: 0.7565 (tp-100) cc_final: 0.7200 (tp-100) REVERT: G 164 MET cc_start: 0.2847 (ttp) cc_final: 0.1837 (tmm) REVERT: L 41 TYR cc_start: 0.8754 (t80) cc_final: 0.8433 (t80) outliers start: 2 outliers final: 0 residues processed: 524 average time/residue: 0.7467 time to fit residues: 454.3944 Evaluate side-chains 403 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.0010 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.8980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 459 ASN A 742 ASN A 947 HIS A1172 ASN ** A1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1102 ASN E 95 GLN E 138 ASN G 21 ASN I 46 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.100859 restraints weight = 38791.716| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.93 r_work: 0.2795 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33698 Z= 0.141 Angle : 0.599 12.960 45858 Z= 0.316 Chirality : 0.045 0.245 5133 Planarity : 0.005 0.064 5659 Dihedral : 13.179 173.489 5164 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.33 % Allowed : 8.42 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: -0.72 (0.13), residues: 3864 helix: -0.05 (0.14), residues: 1338 sheet: -0.66 (0.20), residues: 622 loop : -0.61 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 100 TYR 0.020 0.001 TYR L 41 PHE 0.021 0.001 PHE A 592 TRP 0.013 0.001 TRP B 99 HIS 0.008 0.001 HIS Z 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (33666) covalent geometry : angle 0.58380 / 0.31 (45813) hydrogen bonds : bond 0.04978 / 3.29 ( 1386) hydrogen bonds : angle 5.64448 / 4.03 ( 3902) metal coordination : bond 0.00673 / 0.49 ( 32) metal coordination : angle 4.25384 / 2.84 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 449 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8086 (tppt) cc_final: 0.7881 (tppp) REVERT: A 220 ARG cc_start: 0.7071 (ttt90) cc_final: 0.6858 (ttt90) REVERT: A 540 ASP cc_start: 0.8713 (m-30) cc_final: 0.8493 (m-30) REVERT: A 561 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.9023 (mtt) REVERT: A 735 GLN cc_start: 0.8197 (mp10) cc_final: 0.7409 (mp10) REVERT: A 937 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8017 (p0) REVERT: A 1236 ASN cc_start: 0.7369 (m-40) cc_final: 0.6924 (m-40) REVERT: A 1451 MET cc_start: 0.9162 (mmm) cc_final: 0.8831 (mmm) REVERT: A 1478 GLU cc_start: 0.8221 (mp0) cc_final: 0.8019 (mp0) REVERT: B 967 ARG cc_start: 0.7724 (ttp-110) cc_final: 0.7356 (ttt-90) REVERT: B 1131 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8635 (mtt) REVERT: B 1145 GLN cc_start: 0.8928 (mt0) cc_final: 0.8703 (mt0) REVERT: B 1169 ASP cc_start: 0.8152 (m-30) cc_final: 0.7923 (m-30) REVERT: C 10 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8137 (mtm110) REVERT: D 151 GLU cc_start: 0.3672 (OUTLIER) cc_final: 0.3128 (mm-30) REVERT: E 23 ASP cc_start: 0.8909 (m-30) cc_final: 0.8682 (m-30) REVERT: E 70 ASP cc_start: 0.6811 (m-30) cc_final: 0.6470 (m-30) REVERT: E 116 GLN cc_start: 0.7798 (tp-100) cc_final: 0.7278 (tp-100) REVERT: E 120 ASP cc_start: 0.6855 (m-30) cc_final: 0.6374 (m-30) REVERT: F 90 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8473 (mt) REVERT: F 94 MET cc_start: 0.8675 (mtt) cc_final: 0.8367 (mtt) REVERT: G 164 MET cc_start: 0.2609 (ttp) cc_final: 0.1604 (tmm) REVERT: H 145 MET cc_start: 0.9009 (ptm) cc_final: 0.8671 (ptp) REVERT: I 41 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7855 (t0) REVERT: J 19 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: K 110 LYS cc_start: 0.8636 (ttpt) cc_final: 0.8413 (mtpm) REVERT: L 35 ARG cc_start: 0.8572 (ttp80) cc_final: 0.8340 (ttt-90) REVERT: L 42 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7649 (mmm-85) outliers start: 46 outliers final: 12 residues processed: 470 average time/residue: 0.7024 time to fit residues: 386.9843 Evaluate side-chains 412 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 391 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain B residue 1188 SER Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain L residue 42 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 56 optimal weight: 0.0670 chunk 102 optimal weight: 5.9990 chunk 315 optimal weight: 5.9990 chunk 302 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 258 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 296 optimal weight: 0.0020 chunk 335 optimal weight: 6.9990 overall best weight: 2.4132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS A 950 ASN A1172 ASN A1244 ASN B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 HIS ** B1174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN I 46 GLN K 29 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.146833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.098207 restraints weight = 38734.288| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.03 r_work: 0.2714 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 33698 Z= 0.210 Angle : 0.596 13.385 45858 Z= 0.311 Chirality : 0.046 0.274 5133 Planarity : 0.004 0.059 5659 Dihedral : 13.118 173.983 5164 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.74 % Allowed : 11.02 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: -0.48 (0.13), residues: 3864 helix: 0.30 (0.14), residues: 1354 sheet: -0.77 (0.19), residues: 642 loop : -0.50 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 108 TYR 0.027 0.002 TYR D 109 PHE 0.023 0.002 PHE A 592 TRP 0.014 0.002 TRP B 104 HIS 0.007 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (33666) covalent geometry : angle 0.58155 / 0.31 (45813) hydrogen bonds : bond 0.04536 / 2.99 ( 1386) hydrogen bonds : angle 5.30039 / 3.79 ( 3902) metal coordination : bond 0.00870 / 0.63 ( 32) metal coordination : angle 4.26633 / 2.82 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 414 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7119 (ttt90) cc_final: 0.6867 (ttt90) REVERT: A 291 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7137 (ttm170) REVERT: A 327 ARG cc_start: 0.7074 (mmp80) cc_final: 0.6867 (mmp80) REVERT: A 347 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7913 (mm-30) REVERT: A 514 GLU cc_start: 0.8798 (pt0) cc_final: 0.8528 (pt0) REVERT: A 540 ASP cc_start: 0.8733 (m-30) cc_final: 0.8525 (m-30) REVERT: A 735 GLN cc_start: 0.8169 (mp10) cc_final: 0.7519 (mp10) REVERT: A 937 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7956 (p0) REVERT: A 1059 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8023 (mtt-85) REVERT: A 1236 ASN cc_start: 0.7531 (m-40) cc_final: 0.7140 (m-40) REVERT: B 166 GLU cc_start: 0.8232 (mp0) cc_final: 0.7936 (mp0) REVERT: B 515 ARG cc_start: 0.7861 (ttp-110) cc_final: 0.7617 (ttp-170) REVERT: B 564 SER cc_start: 0.9097 (t) cc_final: 0.8746 (m) REVERT: B 624 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: B 967 ARG cc_start: 0.7727 (ttp-110) cc_final: 0.7366 (ttt-90) REVERT: B 1145 GLN cc_start: 0.8867 (mt0) cc_final: 0.8579 (mt0) REVERT: C 111 GLN cc_start: 0.8244 (pt0) cc_final: 0.8006 (pt0) REVERT: D 151 GLU cc_start: 0.3499 (OUTLIER) cc_final: 0.3010 (mm-30) REVERT: D 167 GLU cc_start: 0.6459 (tp30) cc_final: 0.6001 (tp30) REVERT: E 67 ASP cc_start: 0.7441 (p0) cc_final: 0.7215 (p0) REVERT: E 70 ASP cc_start: 0.6916 (m-30) cc_final: 0.6568 (m-30) REVERT: E 116 GLN cc_start: 0.7795 (tp-100) cc_final: 0.7249 (tp-100) REVERT: F 94 MET cc_start: 0.8707 (mtt) cc_final: 0.8424 (mtt) REVERT: G 104 MET cc_start: 0.3424 (pmm) cc_final: 0.1832 (tpt) REVERT: G 164 MET cc_start: 0.2589 (ttp) cc_final: 0.1508 (tmm) REVERT: H 103 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7582 (pm20) REVERT: I 41 ASN cc_start: 0.8217 (m-40) cc_final: 0.7832 (t0) REVERT: J 19 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: K 110 LYS cc_start: 0.8666 (ttpt) cc_final: 0.8465 (mtpm) REVERT: L 35 ARG cc_start: 0.8554 (ttp80) cc_final: 0.8311 (ttt-90) REVERT: L 42 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7611 (mmm-85) outliers start: 60 outliers final: 22 residues processed: 446 average time/residue: 0.7522 time to fit residues: 392.8853 Evaluate side-chains 430 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 399 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1434 GLU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1188 SER Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 42 ARG Chi-restraints excluded: chain L residue 50 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 387 optimal weight: 50.0000 chunk 18 optimal weight: 0.0370 chunk 42 optimal weight: 0.6980 chunk 189 optimal weight: 3.9990 chunk 368 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 370 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS A1230 GLN B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN H 29 HIS I 32 ASN I 46 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.148711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.102283 restraints weight = 38422.538| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.07 r_work: 0.2826 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33698 Z= 0.124 Angle : 0.533 11.863 45858 Z= 0.279 Chirality : 0.043 0.279 5133 Planarity : 0.004 0.059 5659 Dihedral : 13.023 171.733 5164 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.42 % Allowed : 12.90 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: -0.17 (0.13), residues: 3864 helix: 0.71 (0.14), residues: 1348 sheet: -0.69 (0.19), residues: 631 loop : -0.41 (0.14), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 15 TYR 0.018 0.001 TYR I 37 PHE 0.019 0.001 PHE A 592 TRP 0.012 0.001 TRP A1192 HIS 0.006 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (33666) covalent geometry : angle 0.51910 / 0.28 (45813) hydrogen bonds : bond 0.03823 / 2.51 ( 1386) hydrogen bonds : angle 4.99790 / 3.57 ( 3902) metal coordination : bond 0.00626 / 0.46 ( 32) metal coordination : angle 3.84424 / 2.51 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 425 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7127 (ttt90) cc_final: 0.6839 (ttt90) REVERT: A 223 GLU cc_start: 0.8043 (tp30) cc_final: 0.7330 (tp30) REVERT: A 291 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6980 (ttm170) REVERT: A 347 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7811 (mm-30) REVERT: A 514 GLU cc_start: 0.8674 (pt0) cc_final: 0.8417 (pt0) REVERT: A 540 ASP cc_start: 0.8649 (m-30) cc_final: 0.8423 (m-30) REVERT: A 1236 ASN cc_start: 0.7498 (m-40) cc_final: 0.7093 (m-40) REVERT: A 1262 MET cc_start: 0.5550 (tpt) cc_final: 0.3881 (tmt) REVERT: A 1451 MET cc_start: 0.9174 (mmm) cc_final: 0.8894 (mmm) REVERT: B 166 GLU cc_start: 0.8123 (mp0) cc_final: 0.7809 (mp0) REVERT: B 519 ASP cc_start: 0.8147 (m-30) cc_final: 0.7893 (m-30) REVERT: B 564 SER cc_start: 0.9021 (t) cc_final: 0.8721 (m) REVERT: B 624 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: B 967 ARG cc_start: 0.7709 (ttp-110) cc_final: 0.7290 (ttt-90) REVERT: B 1145 GLN cc_start: 0.8838 (mt0) cc_final: 0.8592 (mt0) REVERT: C 10 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8032 (mtm-85) REVERT: C 85 SER cc_start: 0.9129 (p) cc_final: 0.8869 (t) REVERT: C 111 GLN cc_start: 0.8200 (pt0) cc_final: 0.7929 (pt0) REVERT: D 148 GLU cc_start: 0.2600 (mm-30) cc_final: 0.2201 (mp0) REVERT: D 151 GLU cc_start: 0.3499 (OUTLIER) cc_final: 0.3041 (mm-30) REVERT: E 23 ASP cc_start: 0.8819 (m-30) cc_final: 0.8567 (m-30) REVERT: E 52 ARG cc_start: 0.6477 (mmm-85) cc_final: 0.6244 (mmm-85) REVERT: E 116 GLN cc_start: 0.7714 (tp-100) cc_final: 0.7130 (tp-100) REVERT: G 104 MET cc_start: 0.3495 (pmm) cc_final: 0.2077 (tpt) REVERT: G 164 MET cc_start: 0.2519 (ttp) cc_final: 0.1517 (tmm) REVERT: H 145 MET cc_start: 0.9014 (ptm) cc_final: 0.8652 (ptp) REVERT: I 41 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7899 (t0) REVERT: J 19 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: L 35 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8263 (ttt-90) REVERT: L 42 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7460 (mmm-85) outliers start: 49 outliers final: 14 residues processed: 451 average time/residue: 0.7101 time to fit residues: 375.0641 Evaluate side-chains 419 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 397 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1188 SER Chi-restraints excluded: chain C residue 10 ARG Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain L residue 42 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 209 optimal weight: 4.9990 chunk 203 optimal weight: 0.4980 chunk 188 optimal weight: 3.9990 chunk 278 optimal weight: 8.9990 chunk 186 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 342 optimal weight: 4.9990 chunk 370 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A 780 ASN A 945 ASN A 947 HIS B 188 ASN ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 HIS B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN E 116 GLN G 24 ASN H 130 ASN I 45 GLN I 46 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.147653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.099500 restraints weight = 38667.393| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.97 r_work: 0.2767 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33698 Z= 0.183 Angle : 0.558 12.777 45858 Z= 0.290 Chirality : 0.045 0.340 5133 Planarity : 0.004 0.058 5659 Dihedral : 13.007 172.137 5164 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.97 % Allowed : 13.50 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: -0.09 (0.13), residues: 3864 helix: 0.80 (0.14), residues: 1359 sheet: -0.68 (0.20), residues: 617 loop : -0.38 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 100 TYR 0.020 0.001 TYR I 37 PHE 0.020 0.002 PHE A 592 TRP 0.013 0.001 TRP B 104 HIS 0.006 0.001 HIS A 947 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (33666) covalent geometry : angle 0.54416 / 0.29 (45813) hydrogen bonds : bond 0.03942 / 2.59 ( 1386) hydrogen bonds : angle 4.94348 / 3.53 ( 3902) metal coordination : bond 0.00751 / 0.56 ( 32) metal coordination : angle 3.92662 / 2.55 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 414 time to evaluate : 1.039 Fit side-chains REVERT: A 78 MET cc_start: 0.8497 (ttt) cc_final: 0.8226 (tpp) REVERT: A 223 GLU cc_start: 0.8030 (tp30) cc_final: 0.7356 (tp30) REVERT: A 291 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.7095 (ttm170) REVERT: A 347 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7854 (mm-30) REVERT: A 514 GLU cc_start: 0.8776 (pt0) cc_final: 0.8490 (pt0) REVERT: A 540 ASP cc_start: 0.8710 (m-30) cc_final: 0.8509 (m-30) REVERT: A 735 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7526 (mm-40) REVERT: A 1236 ASN cc_start: 0.7472 (m-40) cc_final: 0.7070 (m-40) REVERT: B 166 GLU cc_start: 0.8290 (mp0) cc_final: 0.7894 (mp0) REVERT: B 375 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7265 (mmt) REVERT: B 515 ARG cc_start: 0.8218 (ttp-170) cc_final: 0.7567 (ttp80) REVERT: B 564 SER cc_start: 0.9064 (t) cc_final: 0.8769 (m) REVERT: B 624 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: B 967 ARG cc_start: 0.7744 (ttp-110) cc_final: 0.7390 (ttt-90) REVERT: B 1131 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8792 (mtt) REVERT: B 1145 GLN cc_start: 0.8867 (mt0) cc_final: 0.8624 (mt0) REVERT: C 85 SER cc_start: 0.9082 (p) cc_final: 0.8857 (t) REVERT: C 111 GLN cc_start: 0.8293 (pt0) cc_final: 0.8046 (pt0) REVERT: D 148 GLU cc_start: 0.2608 (mm-30) cc_final: 0.2205 (mp0) REVERT: D 151 GLU cc_start: 0.3545 (OUTLIER) cc_final: 0.3110 (mm-30) REVERT: G 117 MET cc_start: 0.1027 (mtt) cc_final: 0.0792 (tpt) REVERT: G 164 MET cc_start: 0.2577 (ttp) cc_final: 0.1524 (tmm) REVERT: H 103 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7553 (pm20) REVERT: J 19 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: L 35 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8343 (ttt-90) REVERT: L 42 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7575 (mmm-85) outliers start: 68 outliers final: 22 residues processed: 455 average time/residue: 0.7037 time to fit residues: 376.7047 Evaluate side-chains 436 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 404 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain B residue 1188 SER Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 42 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 23 optimal weight: 10.0000 chunk 365 optimal weight: 0.9980 chunk 210 optimal weight: 0.3980 chunk 270 optimal weight: 1.9990 chunk 350 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 340 optimal weight: 10.0000 chunk 225 optimal weight: 4.9990 chunk 290 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN A 945 ASN A 947 HIS A1172 ASN B 595 HIS B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN E 98 ASN G 24 ASN H 131 ASN I 32 ASN I 46 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.149039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.102485 restraints weight = 38460.569| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.97 r_work: 0.2819 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33698 Z= 0.124 Angle : 0.527 12.132 45858 Z= 0.275 Chirality : 0.043 0.291 5133 Planarity : 0.004 0.058 5659 Dihedral : 12.950 170.553 5164 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.94 % Allowed : 14.72 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 0.10 (0.13), residues: 3864 helix: 1.02 (0.14), residues: 1355 sheet: -0.66 (0.19), residues: 626 loop : -0.28 (0.15), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 100 TYR 0.014 0.001 TYR A 413 PHE 0.018 0.001 PHE A 592 TRP 0.012 0.001 TRP C 49 HIS 0.006 0.001 HIS A 947 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (33666) covalent geometry : angle 0.51404 / 0.27 (45813) hydrogen bonds : bond 0.03593 / 2.35 ( 1386) hydrogen bonds : angle 4.79429 / 3.42 ( 3902) metal coordination : bond 0.00621 / 0.46 ( 32) metal coordination : angle 3.75120 / 2.41 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 424 time to evaluate : 1.292 Fit side-chains REVERT: A 78 MET cc_start: 0.8447 (ttt) cc_final: 0.8197 (tpp) REVERT: A 223 GLU cc_start: 0.7980 (tp30) cc_final: 0.7297 (tp30) REVERT: A 227 ARG cc_start: 0.7607 (ttp-170) cc_final: 0.7201 (mtm-85) REVERT: A 291 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6967 (ttm170) REVERT: A 347 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7798 (mm-30) REVERT: A 540 ASP cc_start: 0.8649 (m-30) cc_final: 0.8414 (m-30) REVERT: A 735 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7493 (mm-40) REVERT: A 1236 ASN cc_start: 0.7472 (m-40) cc_final: 0.7114 (m-40) REVERT: A 1344 MET cc_start: 0.8225 (tpt) cc_final: 0.7857 (tpt) REVERT: A 1451 MET cc_start: 0.9134 (mmm) cc_final: 0.8878 (mmm) REVERT: B 144 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6441 (mp) REVERT: B 166 GLU cc_start: 0.8205 (mp0) cc_final: 0.7867 (mp0) REVERT: B 515 ARG cc_start: 0.8211 (ttp-170) cc_final: 0.7551 (ttp80) REVERT: B 564 SER cc_start: 0.8996 (t) cc_final: 0.8726 (m) REVERT: B 624 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7703 (tm-30) REVERT: B 967 ARG cc_start: 0.7638 (ttp-110) cc_final: 0.7310 (ttt-90) REVERT: B 1084 ASN cc_start: 0.8967 (p0) cc_final: 0.8554 (p0) REVERT: B 1131 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8717 (mtt) REVERT: B 1145 GLN cc_start: 0.8844 (mt0) cc_final: 0.8587 (mt0) REVERT: C 111 GLN cc_start: 0.8221 (pt0) cc_final: 0.7994 (pt0) REVERT: D 148 GLU cc_start: 0.2676 (mm-30) cc_final: 0.2181 (mp0) REVERT: D 151 GLU cc_start: 0.3564 (OUTLIER) cc_final: 0.3158 (mm-30) REVERT: E 3 ASP cc_start: 0.7803 (t0) cc_final: 0.7442 (t0) REVERT: E 23 ASP cc_start: 0.8819 (m-30) cc_final: 0.8594 (m-30) REVERT: E 52 ARG cc_start: 0.6578 (mmm-85) cc_final: 0.6361 (mmm-85) REVERT: E 116 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7316 (tp-100) REVERT: E 120 ASP cc_start: 0.6986 (m-30) cc_final: 0.6746 (m-30) REVERT: G 164 MET cc_start: 0.2384 (ttp) cc_final: 0.1425 (tmm) REVERT: H 103 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7481 (pm20) REVERT: J 19 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: L 35 ARG cc_start: 0.8537 (ttp80) cc_final: 0.8317 (ttt-90) REVERT: L 42 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7436 (mmm-85) outliers start: 67 outliers final: 20 residues processed: 463 average time/residue: 0.7099 time to fit residues: 387.1704 Evaluate side-chains 431 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 401 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain B residue 1188 SER Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain L residue 42 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 294 optimal weight: 9.9990 chunk 305 optimal weight: 0.9980 chunk 180 optimal weight: 0.0030 chunk 248 optimal weight: 0.5980 chunk 264 optimal weight: 6.9990 chunk 251 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 249 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 chunk 317 optimal weight: 5.9990 overall best weight: 1.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 945 ASN A 947 HIS B 595 HIS B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN H 130 ASN I 45 GLN I 46 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.100557 restraints weight = 38549.660| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.94 r_work: 0.2787 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33698 Z= 0.150 Angle : 0.542 12.472 45858 Z= 0.281 Chirality : 0.044 0.262 5133 Planarity : 0.004 0.058 5659 Dihedral : 12.944 170.626 5164 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.74 % Allowed : 15.62 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 0.18 (0.14), residues: 3864 helix: 1.10 (0.14), residues: 1349 sheet: -0.66 (0.19), residues: 636 loop : -0.21 (0.15), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 100 TYR 0.015 0.001 TYR A 413 PHE 0.018 0.001 PHE A 592 TRP 0.013 0.001 TRP C 49 HIS 0.005 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (33666) covalent geometry : angle 0.52945 / 0.28 (45813) hydrogen bonds : bond 0.03628 / 2.38 ( 1386) hydrogen bonds : angle 4.76707 / 3.40 ( 3902) metal coordination : bond 0.00643 / 0.48 ( 32) metal coordination : angle 3.73370 / 2.40 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 412 time to evaluate : 1.305 Fit side-chains REVERT: A 33 ARG cc_start: 0.8200 (ttp-110) cc_final: 0.7931 (ttp-110) REVERT: A 223 GLU cc_start: 0.8059 (tp30) cc_final: 0.7303 (tp30) REVERT: A 227 ARG cc_start: 0.7636 (ttp-170) cc_final: 0.7241 (mtm-85) REVERT: A 291 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.7073 (ttm170) REVERT: A 347 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7832 (mm-30) REVERT: A 514 GLU cc_start: 0.8829 (pt0) cc_final: 0.8479 (pt0) REVERT: A 540 ASP cc_start: 0.8692 (m-30) cc_final: 0.8463 (m-30) REVERT: A 735 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7567 (mm-40) REVERT: A 1236 ASN cc_start: 0.7484 (m-40) cc_final: 0.7117 (m-40) REVERT: A 1292 MET cc_start: 0.8736 (ttp) cc_final: 0.8320 (ttp) REVERT: A 1344 MET cc_start: 0.8290 (tpt) cc_final: 0.7990 (tpt) REVERT: B 144 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6442 (mp) REVERT: B 166 GLU cc_start: 0.8281 (mp0) cc_final: 0.7907 (mp0) REVERT: B 362 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8762 (mp) REVERT: B 515 ARG cc_start: 0.8232 (ttp-170) cc_final: 0.7584 (ttp80) REVERT: B 564 SER cc_start: 0.9022 (t) cc_final: 0.8759 (m) REVERT: B 624 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: B 659 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8066 (pp30) REVERT: B 967 ARG cc_start: 0.7681 (ttp-110) cc_final: 0.7352 (ttt-90) REVERT: B 1084 ASN cc_start: 0.9021 (p0) cc_final: 0.8603 (p0) REVERT: B 1145 GLN cc_start: 0.8883 (mt0) cc_final: 0.8628 (mt0) REVERT: B 1153 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7719 (tt0) REVERT: C 111 GLN cc_start: 0.8248 (pt0) cc_final: 0.8012 (pt0) REVERT: D 148 GLU cc_start: 0.2681 (mm-30) cc_final: 0.2172 (mp0) REVERT: D 151 GLU cc_start: 0.3556 (OUTLIER) cc_final: 0.3119 (mm-30) REVERT: E 3 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7538 (t0) REVERT: E 52 ARG cc_start: 0.6577 (mmm-85) cc_final: 0.6359 (mmm-85) REVERT: E 116 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7266 (tp-100) REVERT: G 164 MET cc_start: 0.2499 (ttp) cc_final: 0.1493 (tmm) REVERT: H 103 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7557 (pm20) REVERT: H 140 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7713 (mmm160) REVERT: J 19 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: K 114 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7170 (pp20) REVERT: L 35 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8317 (ttt-90) outliers start: 60 outliers final: 24 residues processed: 443 average time/residue: 0.7374 time to fit residues: 382.7698 Evaluate side-chains 438 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 401 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1157 ARG Chi-restraints excluded: chain B residue 1188 SER Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 114 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 176 optimal weight: 0.9980 chunk 220 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 324 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 118 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 203 optimal weight: 0.9990 chunk 251 optimal weight: 0.8980 chunk 231 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS B 595 HIS B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 GLN G 24 ASN I 32 ASN I 45 GLN I 46 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.149319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.102233 restraints weight = 38278.343| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.00 r_work: 0.2837 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33698 Z= 0.122 Angle : 0.532 12.019 45858 Z= 0.276 Chirality : 0.043 0.243 5133 Planarity : 0.004 0.058 5659 Dihedral : 12.918 170.006 5164 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.76 % Allowed : 15.82 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 0.26 (0.14), residues: 3864 helix: 1.20 (0.14), residues: 1350 sheet: -0.61 (0.19), residues: 623 loop : -0.20 (0.15), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1031 TYR 0.016 0.001 TYR B 237 PHE 0.017 0.001 PHE A 592 TRP 0.013 0.001 TRP C 49 HIS 0.005 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (33666) covalent geometry : angle 0.51992 / 0.28 (45813) hydrogen bonds : bond 0.03465 / 2.27 ( 1386) hydrogen bonds : angle 4.69779 / 3.35 ( 3902) metal coordination : bond 0.00579 / 0.43 ( 32) metal coordination : angle 3.61469 / 2.30 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 422 time to evaluate : 1.104 Fit side-chains REVERT: A 223 GLU cc_start: 0.7981 (tp30) cc_final: 0.7322 (tp30) REVERT: A 227 ARG cc_start: 0.7581 (ttp-170) cc_final: 0.7161 (mtm-85) REVERT: A 291 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6996 (ttm170) REVERT: A 347 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7784 (mm-30) REVERT: A 514 GLU cc_start: 0.8746 (pt0) cc_final: 0.8412 (pt0) REVERT: A 540 ASP cc_start: 0.8616 (m-30) cc_final: 0.8377 (m-30) REVERT: A 735 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7507 (mm-40) REVERT: A 945 ASN cc_start: 0.7890 (t0) cc_final: 0.7525 (t160) REVERT: A 1008 LYS cc_start: 0.8506 (mmtm) cc_final: 0.7956 (tttm) REVERT: A 1236 ASN cc_start: 0.7477 (m-40) cc_final: 0.7122 (m-40) REVERT: A 1344 MET cc_start: 0.8233 (tpt) cc_final: 0.7913 (tpt) REVERT: B 144 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6447 (mp) REVERT: B 166 GLU cc_start: 0.8215 (mp0) cc_final: 0.7804 (mp0) REVERT: B 362 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8713 (mp) REVERT: B 515 ARG cc_start: 0.8180 (ttp-170) cc_final: 0.7527 (ttp80) REVERT: B 564 SER cc_start: 0.8955 (t) cc_final: 0.8724 (m) REVERT: B 624 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: B 967 ARG cc_start: 0.7624 (ttp-110) cc_final: 0.7299 (ttt-90) REVERT: B 1084 ASN cc_start: 0.8935 (p0) cc_final: 0.8541 (p0) REVERT: B 1131 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8676 (mtt) REVERT: B 1145 GLN cc_start: 0.8802 (mt0) cc_final: 0.8428 (mt0) REVERT: B 1153 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7669 (tt0) REVERT: C 111 GLN cc_start: 0.8208 (pt0) cc_final: 0.7970 (pt0) REVERT: D 148 GLU cc_start: 0.2677 (mm-30) cc_final: 0.2175 (mp0) REVERT: E 3 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7486 (t0) REVERT: E 23 ASP cc_start: 0.8763 (m-30) cc_final: 0.8549 (m-30) REVERT: E 46 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7497 (t0) REVERT: E 52 ARG cc_start: 0.6489 (mmm-85) cc_final: 0.6270 (mmm-85) REVERT: E 116 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7345 (tp-100) REVERT: G 104 MET cc_start: 0.3888 (pmm) cc_final: 0.2535 (ppp) REVERT: G 117 MET cc_start: 0.1083 (OUTLIER) cc_final: 0.0350 (mmm) REVERT: G 164 MET cc_start: 0.2459 (ttp) cc_final: 0.1500 (tmm) REVERT: H 103 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7514 (pm20) REVERT: K 114 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7228 (pp20) REVERT: L 35 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8331 (ttt-90) outliers start: 61 outliers final: 25 residues processed: 457 average time/residue: 0.7297 time to fit residues: 392.0038 Evaluate side-chains 447 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 410 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain B residue 1157 ARG Chi-restraints excluded: chain B residue 1188 SER Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 114 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 194 optimal weight: 1.9990 chunk 228 optimal weight: 0.0870 chunk 22 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 216 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS A1244 ASN B 447 HIS B 595 HIS B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 GLN H 130 ASN I 45 GLN I 56 ASN L 26 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.148078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.100775 restraints weight = 38251.880| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.00 r_work: 0.2803 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33698 Z= 0.179 Angle : 0.567 13.113 45858 Z= 0.291 Chirality : 0.044 0.243 5133 Planarity : 0.004 0.057 5659 Dihedral : 12.940 170.765 5164 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.56 % Allowed : 16.17 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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 (0.14), residues: 3864 helix: 1.14 (0.14), residues: 1349 sheet: -0.64 (0.19), residues: 631 loop : -0.16 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1031 TYR 0.016 0.001 TYR A 413 PHE 0.022 0.002 PHE A 234 TRP 0.014 0.001 TRP C 49 HIS 0.006 0.001 HIS B 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (33666) covalent geometry : angle 0.55445 / 0.29 (45813) hydrogen bonds : bond 0.03667 / 2.40 ( 1386) hydrogen bonds : angle 4.74458 / 3.39 ( 3902) metal coordination : bond 0.00703 / 0.53 ( 32) metal coordination : angle 3.84047 / 2.45 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 420 time to evaluate : 1.184 Fit side-chains REVERT: A 223 GLU cc_start: 0.8023 (tp30) cc_final: 0.7294 (tp30) REVERT: A 227 ARG cc_start: 0.7547 (ttp-170) cc_final: 0.7142 (mtm-85) REVERT: A 291 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.7027 (ttm170) REVERT: A 347 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7838 (mm-30) REVERT: A 514 GLU cc_start: 0.8807 (pt0) cc_final: 0.8485 (pt0) REVERT: A 540 ASP cc_start: 0.8676 (m-30) cc_final: 0.8448 (m-30) REVERT: A 735 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7484 (mm-40) REVERT: A 937 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7997 (p0) REVERT: A 945 ASN cc_start: 0.7876 (t0) cc_final: 0.7485 (t160) REVERT: A 1008 LYS cc_start: 0.8537 (mmtm) cc_final: 0.7994 (tttm) REVERT: A 1059 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7819 (mtt-85) REVERT: A 1228 MET cc_start: 0.7759 (mmm) cc_final: 0.7427 (mmt) REVERT: A 1236 ASN cc_start: 0.7489 (m-40) cc_final: 0.7134 (m-40) REVERT: A 1344 MET cc_start: 0.8273 (tpt) cc_final: 0.7971 (tpt) REVERT: B 144 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6458 (mp) REVERT: B 166 GLU cc_start: 0.8232 (mp0) cc_final: 0.7811 (mp0) REVERT: B 362 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8729 (mp) REVERT: B 515 ARG cc_start: 0.8199 (ttp-170) cc_final: 0.7545 (ttp80) REVERT: B 564 SER cc_start: 0.8976 (t) cc_final: 0.8712 (m) REVERT: B 624 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: B 967 ARG cc_start: 0.7631 (ttp-110) cc_final: 0.7285 (ttt-90) REVERT: B 1084 ASN cc_start: 0.8998 (p0) cc_final: 0.8600 (p0) REVERT: B 1131 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8778 (mtt) REVERT: B 1145 GLN cc_start: 0.8800 (mt0) cc_final: 0.8524 (mt0) REVERT: B 1153 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7753 (tm-30) REVERT: C 111 GLN cc_start: 0.8250 (pt0) cc_final: 0.8045 (pt0) REVERT: D 148 GLU cc_start: 0.2673 (mm-30) cc_final: 0.2177 (mp0) REVERT: D 167 GLU cc_start: 0.6283 (tp30) cc_final: 0.5955 (tp30) REVERT: E 3 ASP cc_start: 0.7818 (t0) cc_final: 0.7480 (t0) REVERT: E 46 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7575 (t0) REVERT: E 116 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7288 (tp-100) REVERT: E 120 ASP cc_start: 0.7068 (m-30) cc_final: 0.6783 (m-30) REVERT: G 117 MET cc_start: 0.1006 (OUTLIER) cc_final: 0.0177 (mmm) REVERT: G 164 MET cc_start: 0.2434 (ttp) cc_final: 0.1471 (tmm) REVERT: H 103 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: H 140 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7662 (mmm160) REVERT: H 145 MET cc_start: 0.9079 (ptm) cc_final: 0.8836 (mtm) REVERT: K 114 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7225 (pp20) REVERT: L 35 ARG cc_start: 0.8566 (ttp80) cc_final: 0.8309 (ttt-90) outliers start: 54 outliers final: 27 residues processed: 450 average time/residue: 0.7143 time to fit residues: 376.8848 Evaluate side-chains 452 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 411 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain B residue 1157 ARG Chi-restraints excluded: chain B residue 1188 SER Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 114 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 161 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 361 optimal weight: 0.9990 chunk 311 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 385 optimal weight: 50.0000 chunk 50 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS A1248 ASN B 447 HIS B 595 HIS ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 GLN I 32 ASN I 45 GLN I 46 GLN I 56 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.147870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.100874 restraints weight = 38659.135| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.08 r_work: 0.2803 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 33698 Z= 0.189 Angle : 0.662 59.199 45858 Z= 0.363 Chirality : 0.044 0.234 5133 Planarity : 0.004 0.057 5659 Dihedral : 12.940 170.769 5164 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.47 % Allowed : 16.57 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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 (0.14), residues: 3864 helix: 1.15 (0.14), residues: 1349 sheet: -0.65 (0.19), residues: 631 loop : -0.15 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1031 TYR 0.016 0.001 TYR A 413 PHE 0.019 0.001 PHE A 592 TRP 0.014 0.001 TRP C 49 HIS 0.007 0.001 HIS B 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (33666) covalent geometry : angle 0.65140 / 0.36 (45813) hydrogen bonds : bond 0.03662 / 2.40 ( 1386) hydrogen bonds : angle 4.76682 / 3.41 ( 3902) metal coordination : bond 0.00665 / 0.50 ( 32) metal coordination : angle 3.85473 / 2.46 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 412 time to evaluate : 1.179 Fit side-chains REVERT: A 223 GLU cc_start: 0.8011 (tp30) cc_final: 0.7294 (tp30) REVERT: A 227 ARG cc_start: 0.7565 (ttp-170) cc_final: 0.7164 (mtm-85) REVERT: A 291 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6990 (ttm170) REVERT: A 347 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7856 (mm-30) REVERT: A 514 GLU cc_start: 0.8823 (pt0) cc_final: 0.8506 (pt0) REVERT: A 540 ASP cc_start: 0.8680 (m-30) cc_final: 0.8458 (m-30) REVERT: A 735 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7491 (mm-40) REVERT: A 937 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7996 (p0) REVERT: A 945 ASN cc_start: 0.7873 (t0) cc_final: 0.7482 (t160) REVERT: A 1008 LYS cc_start: 0.8533 (mmtm) cc_final: 0.7979 (tttm) REVERT: A 1059 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7823 (mtt-85) REVERT: A 1228 MET cc_start: 0.7774 (mmm) cc_final: 0.7440 (mmt) REVERT: A 1236 ASN cc_start: 0.7493 (m-40) cc_final: 0.7139 (m-40) REVERT: A 1344 MET cc_start: 0.8281 (tpt) cc_final: 0.7979 (tpt) REVERT: B 144 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6458 (mp) REVERT: B 166 GLU cc_start: 0.8245 (mp0) cc_final: 0.7810 (mp0) REVERT: B 362 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8718 (mp) REVERT: B 515 ARG cc_start: 0.8196 (ttp-170) cc_final: 0.7545 (ttp80) REVERT: B 564 SER cc_start: 0.8982 (t) cc_final: 0.8713 (m) REVERT: B 624 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: B 967 ARG cc_start: 0.7603 (ttp-110) cc_final: 0.7249 (ttt-90) REVERT: B 1084 ASN cc_start: 0.9005 (p0) cc_final: 0.8591 (p0) REVERT: B 1131 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8798 (mtt) REVERT: B 1145 GLN cc_start: 0.8801 (mt0) cc_final: 0.8524 (mt0) REVERT: B 1153 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7773 (tm-30) REVERT: C 111 GLN cc_start: 0.8275 (pt0) cc_final: 0.8066 (pt0) REVERT: D 148 GLU cc_start: 0.2670 (mm-30) cc_final: 0.2174 (mp0) REVERT: D 167 GLU cc_start: 0.6281 (tp30) cc_final: 0.5952 (tp30) REVERT: E 3 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7494 (t0) REVERT: E 23 ASP cc_start: 0.8823 (m-30) cc_final: 0.8583 (m-30) REVERT: E 46 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7573 (t0) REVERT: G 21 ASN cc_start: 0.8052 (m110) cc_final: 0.7726 (m-40) REVERT: G 117 MET cc_start: 0.0996 (OUTLIER) cc_final: 0.0174 (mmm) REVERT: G 164 MET cc_start: 0.2454 (ttp) cc_final: 0.1468 (tmm) REVERT: H 103 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7601 (pm20) REVERT: H 140 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7684 (mmm160) REVERT: K 114 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7205 (pp20) REVERT: L 35 ARG cc_start: 0.8579 (ttp80) cc_final: 0.8325 (ttt-90) outliers start: 51 outliers final: 27 residues processed: 439 average time/residue: 0.7157 time to fit residues: 368.9095 Evaluate side-chains 442 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 400 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1059 ARG Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 624 GLU Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain B residue 1157 ARG Chi-restraints excluded: chain B residue 1188 SER Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 140 ARG Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 114 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 237 optimal weight: 5.9990 chunk 354 optimal weight: 0.9990 chunk 246 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 230 optimal weight: 0.6980 chunk 340 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 282 optimal weight: 30.0000 chunk 171 optimal weight: 0.0270 chunk 200 optimal weight: 3.9990 chunk 260 optimal weight: 0.5980 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS B 447 HIS B 595 HIS ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 GLN I 32 ASN I 45 GLN I 46 GLN I 56 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.148045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.099811 restraints weight = 38484.802| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.95 r_work: 0.2777 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 33698 Z= 0.189 Angle : 0.662 59.199 45858 Z= 0.363 Chirality : 0.044 0.234 5133 Planarity : 0.004 0.057 5659 Dihedral : 12.940 170.769 5164 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.24 % Allowed : 16.77 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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 (0.14), residues: 3864 helix: 1.15 (0.14), residues: 1349 sheet: -0.65 (0.19), residues: 631 loop : -0.15 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1031 TYR 0.016 0.001 TYR A 413 PHE 0.019 0.001 PHE A 592 TRP 0.014 0.001 TRP C 49 HIS 0.007 0.001 HIS B 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (33666) covalent geometry : angle 0.65140 / 0.36 (45813) hydrogen bonds : bond 0.03662 / 2.40 ( 1386) hydrogen bonds : angle 4.76682 / 3.41 ( 3902) metal coordination : bond 0.00665 / 0.50 ( 32) metal coordination : angle 3.85473 / 2.46 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11389.00 seconds wall clock time: 194 minutes 30.34 seconds (11670.34 seconds total)