Starting phenix.real_space_refine on Mon Sep 14 20:25:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ol0_12974/09_2026/7ol0_12974.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ol0_12974/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ol0_12974/09_2026/7ol0_12974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ol0_12974/09_2026/7ol0_12974.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ol0_12974/09_2026/7ol0_12974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ol0_12974/09_2026/7ol0_12974.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ol0_12974/09_2026/7ol0_12974.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ol0_12974/09_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): 0.24s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 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: 6.60, per 1000 atoms: 0.20 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: 3.16 Conformation dependent library (CDL) restraints added in 1.3 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: 4.02 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: 9.57 Time building geometry restraints manager: 3.95 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: 45194 3.11 - 6.21: 571 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: 19802 35.42 - 70.83: 584 70.83 - 106.25: 46 106.25 - 141.67: 0 141.67 - 177.09: 1 Dihedral angle restraints: 20433 sinusoidal: 9057 harmonic: 11376 Sorted by residual: dihedral pdb=" C4' G P 36 " pdb=" C3' G P 36 " pdb=" C2' G P 36 " pdb=" C1' G P 36 " ideal model delta sinusoidal sigma weight residual 36.34 -34.86 71.21 1 3.10e+00 1.04e-01 6.77e+02 dihedral pdb=" C4' G P 35 " pdb=" C3' G P 35 " pdb=" C2' G P 35 " pdb=" C1' G P 35 " ideal model delta sinusoidal sigma weight residual 36.35 -34.84 71.18 1 3.10e+00 1.04e-01 6.77e+02 dihedral pdb=" C4' A P 34 " pdb=" C3' A P 34 " pdb=" C2' A P 34 " pdb=" C1' A P 34 " ideal model delta sinusoidal sigma weight residual 36.34 -34.60 70.95 1 3.10e+00 1.04e-01 6.73e+02 ... (remaining 20430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 4784 0.108 - 0.216: 324 0.216 - 0.325: 20 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: 1.620 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 39.260 Find NCS groups from input model: 0.340 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:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.750 ------------------------------------------------------------------------------- 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= 0.426 Angle : 0.906 15.529 45858 Z= 0.516 Chirality : 0.060 0.541 5133 Planarity : 0.006 0.075 5659 Dihedral : 15.953 177.086 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 0.89471 / 0.52 (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 : 1.202 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: 0.8568 time to fit residues: 521.2846 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 : 1.293 ------------------------------------------------------------------------------- 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 ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.148813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.100456 restraints weight = 38775.091| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.96 r_work: 0.2790 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33698 Z= 0.147 Angle : 0.643 14.472 45858 Z= 0.334 Chirality : 0.052 1.303 5133 Planarity : 0.005 0.064 5659 Dihedral : 13.349 174.262 5164 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.42 % Allowed : 8.44 % Favored : 90.14 % 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: -0.73 (0.13), residues: 3864 helix: -0.06 (0.14), residues: 1338 sheet: -0.65 (0.20), residues: 619 loop : -0.62 (0.14), residues: 1907 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 0.014 0.001 TRP B 99 HIS 0.007 0.001 HIS Z 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (33666) covalent geometry : angle 0.62903 / 0.33 (45813) hydrogen bonds : bond 0.04845 / 3.21 ( 1386) hydrogen bonds : angle 5.64415 / 4.03 ( 3902) metal coordination : bond 0.00689 / 0.50 ( 32) metal coordination : angle 4.29948 / 2.87 ( 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 498 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 449 time to evaluate : 1.309 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7073 (ttt90) cc_final: 0.6868 (ttt90) REVERT: A 514 GLU cc_start: 0.8812 (pt0) cc_final: 0.8448 (pt0) REVERT: A 540 ASP cc_start: 0.8720 (m-30) cc_final: 0.8513 (m-30) REVERT: A 561 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.9032 (mtt) REVERT: A 735 GLN cc_start: 0.8192 (mp10) cc_final: 0.7402 (mp10) REVERT: A 937 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8014 (p0) REVERT: A 1236 ASN cc_start: 0.7370 (m-40) cc_final: 0.6925 (m-40) REVERT: A 1451 MET cc_start: 0.9168 (mmm) cc_final: 0.8833 (mmm) REVERT: A 1478 GLU cc_start: 0.8195 (mp0) cc_final: 0.7979 (mp0) REVERT: B 515 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.7475 (ttp-170) REVERT: B 967 ARG cc_start: 0.7750 (ttp-110) cc_final: 0.7359 (ttt-90) REVERT: B 1131 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8643 (mtt) REVERT: B 1145 GLN cc_start: 0.8928 (mt0) cc_final: 0.8705 (mt0) REVERT: B 1169 ASP cc_start: 0.8165 (m-30) cc_final: 0.7930 (m-30) REVERT: C 10 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8157 (mtm110) REVERT: D 151 GLU cc_start: 0.3654 (OUTLIER) cc_final: 0.3096 (mm-30) REVERT: E 23 ASP cc_start: 0.8913 (m-30) cc_final: 0.8683 (m-30) REVERT: E 70 ASP cc_start: 0.6813 (m-30) cc_final: 0.6470 (m-30) REVERT: E 116 GLN cc_start: 0.7801 (tp-100) cc_final: 0.7274 (tp-100) REVERT: E 120 ASP cc_start: 0.6871 (m-30) cc_final: 0.6379 (m-30) REVERT: F 90 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8472 (mt) REVERT: F 94 MET cc_start: 0.8661 (mtt) cc_final: 0.8347 (mtt) REVERT: G 164 MET cc_start: 0.2630 (ttp) cc_final: 0.1605 (tmm) REVERT: H 145 MET cc_start: 0.9019 (ptm) cc_final: 0.8686 (ptp) REVERT: I 41 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7843 (t0) REVERT: J 19 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: K 110 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8424 (mtpm) REVERT: L 35 ARG cc_start: 0.8572 (ttp80) cc_final: 0.8342 (ttt-90) REVERT: L 42 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7665 (mmm-85) outliers start: 49 outliers final: 12 residues processed: 471 average time/residue: 0.8280 time to fit residues: 457.3477 Evaluate side-chains 413 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 392 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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: 0.9980 chunk 102 optimal weight: 0.9980 chunk 315 optimal weight: 4.9990 chunk 302 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 258 optimal weight: 9.9990 chunk 179 optimal weight: 0.6980 chunk 296 optimal weight: 0.0030 chunk 335 optimal weight: 0.6980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS A 950 ASN B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN I 32 ASN I 46 GLN K 29 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.149458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.100754 restraints weight = 38723.612| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.94 r_work: 0.2795 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33698 Z= 0.123 Angle : 0.571 11.630 45858 Z= 0.295 Chirality : 0.046 0.627 5133 Planarity : 0.004 0.059 5659 Dihedral : 13.249 172.460 5164 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.33 % Allowed : 11.02 % Favored : 87.65 % 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: -0.40 (0.13), residues: 3864 helix: 0.39 (0.14), residues: 1363 sheet: -0.63 (0.20), residues: 609 loop : -0.53 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 100 TYR 0.030 0.001 TYR D 109 PHE 0.019 0.001 PHE A 592 TRP 0.012 0.001 TRP B 99 HIS 0.007 0.001 HIS A 947 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (33666) covalent geometry : angle 0.55814 / 0.29 (45813) hydrogen bonds : bond 0.04097 / 2.69 ( 1386) hydrogen bonds : angle 5.18616 / 3.70 ( 3902) metal coordination : bond 0.00620 / 0.45 ( 32) metal coordination : angle 3.82488 / 2.51 ( 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 462 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 416 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8346 (mmtp) cc_final: 0.8063 (mmmm) REVERT: A 291 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7094 (ttm170) REVERT: A 347 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7910 (mm-30) REVERT: A 540 ASP cc_start: 0.8738 (m-30) cc_final: 0.8520 (m-30) REVERT: A 1236 ASN cc_start: 0.7452 (m-40) cc_final: 0.7074 (m-40) REVERT: A 1262 MET cc_start: 0.5527 (tpt) cc_final: 0.3670 (tmt) REVERT: A 1451 MET cc_start: 0.9143 (mmm) cc_final: 0.8920 (mmm) REVERT: A 1478 GLU cc_start: 0.8197 (mp0) cc_final: 0.7991 (mp0) REVERT: B 166 GLU cc_start: 0.8205 (mp0) cc_final: 0.7931 (mp0) REVERT: B 519 ASP cc_start: 0.8344 (m-30) cc_final: 0.8098 (m-30) REVERT: B 624 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: B 967 ARG cc_start: 0.7759 (ttp-110) cc_final: 0.7374 (ttt-90) REVERT: B 1131 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8538 (mtt) REVERT: B 1145 GLN cc_start: 0.8873 (mt0) cc_final: 0.8545 (mt0) REVERT: B 1169 ASP cc_start: 0.8197 (m-30) cc_final: 0.7995 (m-30) REVERT: C 10 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8211 (mtm110) REVERT: D 151 GLU cc_start: 0.3501 (OUTLIER) cc_final: 0.3023 (mm-30) REVERT: E 116 GLN cc_start: 0.7743 (tp-100) cc_final: 0.7180 (tp-100) REVERT: F 94 MET cc_start: 0.8668 (mtt) cc_final: 0.8400 (mtt) REVERT: G 104 MET cc_start: 0.3372 (pmm) cc_final: 0.2015 (tpt) REVERT: G 164 MET cc_start: 0.2716 (ttp) cc_final: 0.1675 (tmm) REVERT: H 145 MET cc_start: 0.9077 (ptm) cc_final: 0.8742 (ptp) REVERT: J 19 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: L 35 ARG cc_start: 0.8564 (ttp80) cc_final: 0.8235 (ttt-90) REVERT: L 42 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7576 (mmm-85) outliers start: 46 outliers final: 12 residues processed: 440 average time/residue: 0.8434 time to fit residues: 434.4603 Evaluate side-chains 415 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 395 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 167 GLN 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 1131 MET 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 F residue 90 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 96 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 387 optimal weight: 50.0000 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 368 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 370 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 179 optimal weight: 10.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 780 ASN A 945 ASN A 947 HIS A1230 GLN B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 HIS H 130 ASN I 18 GLN I 46 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.148067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.100825 restraints weight = 38488.758| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.08 r_work: 0.2809 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33698 Z= 0.164 Angle : 0.568 12.246 45858 Z= 0.293 Chirality : 0.047 0.550 5133 Planarity : 0.004 0.059 5659 Dihedral : 13.238 172.902 5164 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.62 % Allowed : 12.67 % Favored : 85.71 % 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: -0.14 (0.13), residues: 3864 helix: 0.70 (0.14), residues: 1354 sheet: -0.60 (0.20), residues: 631 loop : -0.39 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 100 TYR 0.018 0.001 TYR I 37 PHE 0.020 0.001 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 0.00375 / 0.16 (33666) covalent geometry : angle 0.55501 / 0.29 (45813) hydrogen bonds : bond 0.03971 / 2.61 ( 1386) hydrogen bonds : angle 5.00832 / 3.58 ( 3902) metal coordination : bond 0.00716 / 0.53 ( 32) metal coordination : angle 3.89208 / 2.54 ( 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 471 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 415 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.8447 (ttt) cc_final: 0.8186 (tpp) REVERT: A 291 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.7028 (ttm170) REVERT: A 347 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7871 (mm-30) REVERT: A 514 GLU cc_start: 0.8776 (pt0) cc_final: 0.8500 (pt0) REVERT: A 540 ASP cc_start: 0.8687 (m-30) cc_final: 0.8479 (m-30) REVERT: A 735 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7487 (mp10) REVERT: A 945 ASN cc_start: 0.7873 (t0) cc_final: 0.7545 (t160) REVERT: A 1236 ASN cc_start: 0.7497 (m-40) cc_final: 0.7095 (m-40) REVERT: B 166 GLU cc_start: 0.8227 (mp0) cc_final: 0.7815 (mp0) REVERT: B 515 ARG cc_start: 0.8177 (ttp-170) cc_final: 0.7597 (ttp80) REVERT: B 564 SER cc_start: 0.9031 (t) cc_final: 0.8765 (m) REVERT: B 624 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7687 (tm-30) REVERT: B 967 ARG cc_start: 0.7668 (ttp-110) cc_final: 0.7397 (ttt-90) REVERT: B 1131 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8501 (mtt) REVERT: B 1145 GLN cc_start: 0.8874 (mt0) cc_final: 0.8633 (mt0) REVERT: C 85 SER cc_start: 0.9080 (p) cc_final: 0.8829 (t) REVERT: D 148 GLU cc_start: 0.2676 (mm-30) cc_final: 0.2164 (mp0) REVERT: D 151 GLU cc_start: 0.3534 (OUTLIER) cc_final: 0.3113 (mm-30) REVERT: E 23 ASP cc_start: 0.8848 (m-30) cc_final: 0.8623 (m-30) REVERT: E 116 GLN cc_start: 0.7720 (tp-100) cc_final: 0.7145 (tp-100) REVERT: E 120 ASP cc_start: 0.7048 (m-30) cc_final: 0.6647 (m-30) REVERT: G 104 MET cc_start: 0.3399 (pmm) cc_final: 0.1997 (tpt) REVERT: G 164 MET cc_start: 0.2588 (ttp) cc_final: 0.1594 (tmm) REVERT: H 103 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: H 145 MET cc_start: 0.9064 (ptm) cc_final: 0.8762 (ptp) REVERT: J 19 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: L 35 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8191 (ttt-90) REVERT: L 42 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7540 (mmm-85) outliers start: 56 outliers final: 20 residues processed: 442 average time/residue: 0.8193 time to fit residues: 422.7476 Evaluate side-chains 421 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 392 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 637 MET Chi-restraints excluded: chain A residue 712 ASP 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 209 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 186 optimal weight: 0.1980 chunk 75 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 342 optimal weight: 3.9990 chunk 370 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN A 673 GLN A 947 HIS B 595 HIS B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 GLN G 24 ASN H 29 HIS I 32 ASN I 46 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.148495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.101790 restraints weight = 38726.238| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.08 r_work: 0.2791 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 33698 Z= 0.156 Angle : 0.556 12.599 45858 Z= 0.286 Chirality : 0.046 0.454 5133 Planarity : 0.004 0.058 5659 Dihedral : 13.237 172.520 5164 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.82 % Allowed : 13.48 % Favored : 84.70 % 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: -0.00 (0.13), residues: 3864 helix: 0.85 (0.14), residues: 1353 sheet: -0.61 (0.19), residues: 631 loop : -0.31 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 100 TYR 0.017 0.001 TYR I 37 PHE 0.020 0.001 PHE A 592 TRP 0.012 0.001 TRP A1192 HIS 0.006 0.001 HIS A 947 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (33666) covalent geometry : angle 0.54234 / 0.29 (45813) hydrogen bonds : bond 0.03811 / 2.50 ( 1386) hydrogen bonds : angle 4.89825 / 3.50 ( 3902) metal coordination : bond 0.00693 / 0.52 ( 32) metal coordination : angle 3.90103 / 2.53 ( 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 473 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 410 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.8478 (ttt) cc_final: 0.8255 (tpp) REVERT: A 291 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.7070 (ttm170) REVERT: A 347 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7851 (mm-30) REVERT: A 514 GLU cc_start: 0.8776 (pt0) cc_final: 0.8562 (pt0) REVERT: A 540 ASP cc_start: 0.8678 (m-30) cc_final: 0.8474 (m-30) REVERT: A 735 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7488 (mm-40) REVERT: A 945 ASN cc_start: 0.7901 (t0) cc_final: 0.7438 (t160) REVERT: A 1236 ASN cc_start: 0.7529 (m-40) cc_final: 0.7125 (m-40) REVERT: A 1451 MET cc_start: 0.9143 (mmm) cc_final: 0.8891 (mmm) REVERT: B 166 GLU cc_start: 0.8263 (mp0) cc_final: 0.7874 (mp0) REVERT: B 515 ARG cc_start: 0.8217 (ttp-170) cc_final: 0.7582 (ttp80) REVERT: B 564 SER cc_start: 0.9015 (t) cc_final: 0.8751 (m) REVERT: B 624 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: B 967 ARG cc_start: 0.7671 (ttp-110) cc_final: 0.7421 (ttt-90) REVERT: B 1084 ASN cc_start: 0.8998 (p0) cc_final: 0.8586 (p0) REVERT: B 1131 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8514 (mtt) REVERT: B 1145 GLN cc_start: 0.8868 (mt0) cc_final: 0.8615 (mt0) REVERT: D 148 GLU cc_start: 0.2679 (mm-30) cc_final: 0.2168 (mp0) REVERT: D 151 GLU cc_start: 0.3540 (OUTLIER) cc_final: 0.3104 (mm-30) REVERT: E 116 GLN cc_start: 0.7683 (tp-100) cc_final: 0.7119 (tp-100) REVERT: E 120 ASP cc_start: 0.6993 (m-30) cc_final: 0.6588 (m-30) REVERT: G 164 MET cc_start: 0.2547 (ttp) cc_final: 0.1528 (tmm) REVERT: H 103 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7530 (pm20) REVERT: H 145 MET cc_start: 0.9091 (ptm) cc_final: 0.8804 (ptp) REVERT: J 19 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: L 35 ARG cc_start: 0.8500 (ttp80) cc_final: 0.8288 (ttt-90) REVERT: L 42 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7534 (mmm-85) outliers start: 63 outliers final: 24 residues processed: 447 average time/residue: 0.7941 time to fit residues: 416.9073 Evaluate side-chains 424 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 391 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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 637 MET Chi-restraints excluded: chain A residue 712 ASP 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 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 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 I residue 32 ASN 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: 9.9990 chunk 365 optimal weight: 0.8980 chunk 210 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 chunk 350 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 163 optimal weight: 0.1980 chunk 57 optimal weight: 9.9990 chunk 340 optimal weight: 9.9990 chunk 225 optimal weight: 4.9990 chunk 290 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 947 HIS A1172 ASN B 188 ASN B 595 HIS B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN G 24 ASN H 130 ASN I 18 GLN I 45 GLN I 46 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.148201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.101412 restraints weight = 38531.524| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.10 r_work: 0.2787 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33698 Z= 0.168 Angle : 0.560 12.995 45858 Z= 0.288 Chirality : 0.046 0.415 5133 Planarity : 0.004 0.058 5659 Dihedral : 13.214 172.527 5164 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.91 % Allowed : 14.49 % Favored : 83.60 % 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: 0.06 (0.13), residues: 3864 helix: 0.94 (0.14), residues: 1354 sheet: -0.64 (0.19), residues: 626 loop : -0.27 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 15 TYR 0.016 0.001 TYR A 413 PHE 0.020 0.001 PHE A 592 TRP 0.012 0.001 TRP B 104 HIS 0.005 0.001 HIS A 947 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (33666) covalent geometry : angle 0.54671 / 0.29 (45813) hydrogen bonds : bond 0.03795 / 2.49 ( 1386) hydrogen bonds : angle 4.85226 / 3.47 ( 3902) metal coordination : bond 0.00706 / 0.53 ( 32) metal coordination : angle 3.92032 / 2.54 ( 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 473 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 407 time to evaluate : 1.301 Fit side-chains REVERT: A 33 ARG cc_start: 0.8186 (ttp-110) cc_final: 0.7897 (ttp-110) REVERT: A 78 MET cc_start: 0.8473 (ttt) cc_final: 0.8260 (tpp) REVERT: A 291 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.7046 (ttm170) REVERT: A 347 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7848 (mm-30) REVERT: A 540 ASP cc_start: 0.8659 (m-30) cc_final: 0.8444 (m-30) REVERT: A 735 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7560 (mm-40) REVERT: A 937 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7969 (p0) REVERT: A 945 ASN cc_start: 0.7913 (t0) cc_final: 0.7477 (t160) REVERT: A 1160 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7868 (mtp85) REVERT: A 1236 ASN cc_start: 0.7436 (m-40) cc_final: 0.7051 (m-40) REVERT: A 1451 MET cc_start: 0.9126 (mmm) cc_final: 0.8899 (mmm) REVERT: B 166 GLU cc_start: 0.8252 (mp0) cc_final: 0.7930 (mp0) REVERT: B 375 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7111 (mmt) REVERT: B 515 ARG cc_start: 0.8219 (ttp-170) cc_final: 0.7574 (ttp80) REVERT: B 564 SER cc_start: 0.9006 (t) cc_final: 0.8755 (m) REVERT: B 624 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7769 (tm-30) REVERT: B 967 ARG cc_start: 0.7677 (ttp-110) cc_final: 0.7424 (ttt-90) REVERT: B 1084 ASN cc_start: 0.8996 (p0) cc_final: 0.8601 (p0) REVERT: B 1131 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8556 (mtt) REVERT: B 1145 GLN cc_start: 0.8867 (mt0) cc_final: 0.8613 (mt0) REVERT: D 148 GLU cc_start: 0.2677 (mm-30) cc_final: 0.2168 (mp0) REVERT: D 151 GLU cc_start: 0.3550 (OUTLIER) cc_final: 0.3115 (mm-30) REVERT: E 3 ASP cc_start: 0.7915 (t0) cc_final: 0.7646 (t0) REVERT: E 23 ASP cc_start: 0.8845 (m-30) cc_final: 0.8615 (m-30) REVERT: E 116 GLN cc_start: 0.7691 (tp-100) cc_final: 0.7087 (tp-100) REVERT: E 120 ASP cc_start: 0.7050 (m-30) cc_final: 0.6734 (m-30) REVERT: G 117 MET cc_start: 0.1022 (mtt) cc_final: 0.0782 (tpt) REVERT: G 164 MET cc_start: 0.2381 (ttp) cc_final: 0.1426 (tmm) REVERT: H 103 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7514 (pm20) REVERT: J 19 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: L 35 ARG cc_start: 0.8536 (ttp80) cc_final: 0.8322 (ttt-90) REVERT: L 42 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7508 (mmm-85) outliers start: 66 outliers final: 27 residues processed: 449 average time/residue: 0.8214 time to fit residues: 432.3406 Evaluate side-chains 437 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 399 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 637 MET Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 97 ASP 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 375 MET 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 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 G residue 131 MET 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 20 THR 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: 6.9990 chunk 305 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 264 optimal weight: 5.9990 chunk 251 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 249 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 317 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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** I 32 ASN I 46 GLN L 26 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.147641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.100799 restraints weight = 38702.908| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.09 r_work: 0.2774 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33698 Z= 0.187 Angle : 0.574 13.356 45858 Z= 0.294 Chirality : 0.046 0.402 5133 Planarity : 0.004 0.057 5659 Dihedral : 13.204 172.861 5164 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.97 % Allowed : 14.84 % Favored : 83.20 % 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: 0.97 (0.14), residues: 1355 sheet: -0.67 (0.19), residues: 630 loop : -0.24 (0.15), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 15 TYR 0.017 0.001 TYR A 413 PHE 0.021 0.002 PHE A 592 TRP 0.013 0.001 TRP B 104 HIS 0.005 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (33666) covalent geometry : angle 0.56056 / 0.29 (45813) hydrogen bonds : bond 0.03838 / 2.52 ( 1386) hydrogen bonds : angle 4.83769 / 3.46 ( 3902) metal coordination : bond 0.00750 / 0.56 ( 32) metal coordination : angle 4.03022 / 2.61 ( 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 477 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 409 time to evaluate : 1.273 Fit side-chains REVERT: A 33 ARG cc_start: 0.8194 (ttp-110) cc_final: 0.7914 (ttp-110) REVERT: A 291 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.7072 (ttm170) REVERT: A 347 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7837 (mm-30) REVERT: A 514 GLU cc_start: 0.8800 (pt0) cc_final: 0.8454 (pt0) REVERT: A 540 ASP cc_start: 0.8676 (m-30) cc_final: 0.8464 (m-30) REVERT: A 735 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7606 (mm-40) REVERT: A 937 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7984 (p0) REVERT: A 945 ASN cc_start: 0.7932 (t0) cc_final: 0.7496 (t160) REVERT: A 1236 ASN cc_start: 0.7441 (m-40) cc_final: 0.7048 (m-40) REVERT: B 144 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6410 (mp) REVERT: B 166 GLU cc_start: 0.8281 (mp0) cc_final: 0.7905 (mp0) REVERT: B 375 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7228 (mmt) REVERT: B 515 ARG cc_start: 0.8225 (ttp-170) cc_final: 0.7624 (ttp80) REVERT: B 564 SER cc_start: 0.9023 (t) cc_final: 0.8770 (m) REVERT: B 624 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7768 (tm-30) REVERT: B 967 ARG cc_start: 0.7665 (ttp-110) cc_final: 0.7415 (ttt-90) REVERT: B 1145 GLN cc_start: 0.8884 (mt0) cc_final: 0.8628 (mt0) REVERT: D 148 GLU cc_start: 0.2679 (mm-30) cc_final: 0.2173 (mp0) REVERT: D 151 GLU cc_start: 0.3559 (OUTLIER) cc_final: 0.3124 (mm-30) REVERT: E 3 ASP cc_start: 0.7960 (t0) cc_final: 0.7641 (t0) REVERT: E 116 GLN cc_start: 0.7700 (tp-100) cc_final: 0.7076 (tp-100) REVERT: E 120 ASP cc_start: 0.7244 (m-30) cc_final: 0.6933 (m-30) REVERT: G 117 MET cc_start: 0.0979 (mtt) cc_final: 0.0753 (tpt) REVERT: G 164 MET cc_start: 0.2392 (ttp) cc_final: 0.1432 (tmm) REVERT: H 103 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: H 140 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7743 (mmm160) REVERT: J 19 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: L 35 ARG cc_start: 0.8566 (ttp80) cc_final: 0.8304 (ttt-90) REVERT: L 42 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7535 (mmm-85) outliers start: 68 outliers final: 27 residues processed: 450 average time/residue: 0.8142 time to fit residues: 429.0773 Evaluate side-chains 437 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 398 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 637 MET Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 937 ASP 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 277 MET Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 344 VAL 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 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 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 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 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 L residue 42 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 176 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 324 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 118 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 203 optimal weight: 0.8980 chunk 251 optimal weight: 0.8980 chunk 231 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN A 947 HIS B 595 HIS B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN I 18 GLN I 32 ASN 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 = 0.3724 r_free = 0.3724 target = 0.149172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.101932 restraints weight = 38470.674| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.08 r_work: 0.2791 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33698 Z= 0.122 Angle : 0.539 12.109 45858 Z= 0.277 Chirality : 0.044 0.366 5133 Planarity : 0.004 0.058 5659 Dihedral : 13.143 170.828 5164 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.45 % Allowed : 15.79 % Favored : 82.76 % 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: 0.22 (0.14), residues: 3864 helix: 1.16 (0.14), residues: 1349 sheet: -0.67 (0.19), residues: 626 loop : -0.21 (0.15), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1031 TYR 0.014 0.001 TYR A 413 PHE 0.018 0.001 PHE A 592 TRP 0.013 0.001 TRP C 49 HIS 0.006 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (33666) covalent geometry : angle 0.52677 / 0.28 (45813) hydrogen bonds : bond 0.03472 / 2.27 ( 1386) hydrogen bonds : angle 4.70308 / 3.36 ( 3902) metal coordination : bond 0.00603 / 0.45 ( 32) metal coordination : angle 3.72063 / 2.37 ( 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 469 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 419 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: A 291 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6977 (ttm170) REVERT: A 347 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7797 (mm-30) REVERT: A 514 GLU cc_start: 0.8746 (pt0) cc_final: 0.8420 (pt0) REVERT: A 540 ASP cc_start: 0.8603 (m-30) cc_final: 0.8351 (m-30) REVERT: A 735 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7519 (mm-40) REVERT: A 1008 LYS cc_start: 0.8548 (mmtm) cc_final: 0.8006 (tttm) REVERT: A 1236 ASN cc_start: 0.7465 (m-40) cc_final: 0.7101 (m-40) REVERT: A 1451 MET cc_start: 0.9097 (mmm) cc_final: 0.8813 (mmm) REVERT: B 144 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6430 (mp) REVERT: B 166 GLU cc_start: 0.8264 (mp0) cc_final: 0.7860 (mp0) REVERT: B 362 LEU cc_start: 0.9021 (mt) cc_final: 0.8688 (mp) REVERT: B 375 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7154 (mmt) REVERT: B 515 ARG cc_start: 0.8187 (ttp-170) cc_final: 0.7576 (ttp80) REVERT: B 564 SER cc_start: 0.8957 (t) cc_final: 0.8744 (m) REVERT: B 624 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: B 967 ARG cc_start: 0.7645 (ttp-110) cc_final: 0.7414 (ttt-90) REVERT: B 1084 ASN cc_start: 0.8940 (p0) cc_final: 0.8534 (p0) REVERT: B 1145 GLN cc_start: 0.8822 (mt0) cc_final: 0.8545 (mt0) REVERT: B 1153 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7657 (tt0) REVERT: C 109 GLU cc_start: 0.7714 (tt0) cc_final: 0.7349 (tt0) REVERT: D 148 GLU cc_start: 0.2671 (mm-30) cc_final: 0.2166 (mp0) REVERT: E 3 ASP cc_start: 0.7741 (t0) cc_final: 0.7381 (t0) REVERT: E 23 ASP cc_start: 0.8829 (m-30) cc_final: 0.8602 (m-30) REVERT: E 116 GLN cc_start: 0.7685 (tp-100) cc_final: 0.7108 (tp-100) REVERT: E 120 ASP cc_start: 0.7223 (m-30) cc_final: 0.6820 (m-30) REVERT: G 164 MET cc_start: 0.2468 (ttp) cc_final: 0.1501 (tmm) REVERT: L 35 ARG cc_start: 0.8558 (ttp80) cc_final: 0.8284 (ttt-90) outliers start: 50 outliers final: 23 residues processed: 448 average time/residue: 0.8376 time to fit residues: 439.5490 Evaluate side-chains 418 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 389 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ARG 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 488 VAL Chi-restraints excluded: chain A residue 637 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 375 MET Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 624 GLU 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 1188 SER Chi-restraints excluded: chain E residue 27 LEU 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 62 SER Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 16 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 194 optimal weight: 7.9990 chunk 228 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 216 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 138 optimal weight: 0.3980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 595 HIS B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS 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 = 0.3724 r_free = 0.3724 target = 0.149144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.101850 restraints weight = 38374.187| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.05 r_work: 0.2827 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33698 Z= 0.136 Angle : 0.553 12.406 45858 Z= 0.283 Chirality : 0.044 0.355 5133 Planarity : 0.004 0.057 5659 Dihedral : 13.125 170.894 5164 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.42 % Allowed : 16.08 % Favored : 82.50 % 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: 0.27 (0.14), residues: 3864 helix: 1.20 (0.14), residues: 1351 sheet: -0.64 (0.19), residues: 621 loop : -0.17 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1031 TYR 0.015 0.001 TYR A 413 PHE 0.017 0.001 PHE A 592 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 0.00308 / 0.14 (33666) covalent geometry : angle 0.54107 / 0.28 (45813) hydrogen bonds : bond 0.03485 / 2.28 ( 1386) hydrogen bonds : angle 4.67624 / 3.34 ( 3902) metal coordination : bond 0.00606 / 0.46 ( 32) metal coordination : angle 3.69536 / 2.35 ( 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 453 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 404 time to evaluate : 1.612 Fit side-chains REVERT: A 291 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.7027 (ttm170) REVERT: A 347 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7868 (mm-30) REVERT: A 540 ASP cc_start: 0.8600 (m-30) cc_final: 0.8350 (m-30) REVERT: A 1008 LYS cc_start: 0.8558 (mmtm) cc_final: 0.8019 (tttm) REVERT: A 1236 ASN cc_start: 0.7462 (m-40) cc_final: 0.7103 (m-40) REVERT: A 1247 PHE cc_start: 0.7192 (p90) cc_final: 0.6478 (p90) REVERT: A 1451 MET cc_start: 0.9078 (mmm) cc_final: 0.8817 (mmm) REVERT: B 144 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6436 (mp) REVERT: B 166 GLU cc_start: 0.8283 (mp0) cc_final: 0.7869 (mp0) REVERT: B 362 LEU cc_start: 0.9011 (mt) cc_final: 0.8659 (mp) REVERT: B 375 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7061 (mmt) REVERT: B 515 ARG cc_start: 0.8193 (ttp-170) cc_final: 0.7578 (ttp80) REVERT: B 624 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: B 967 ARG cc_start: 0.7643 (ttp-110) cc_final: 0.7398 (ttt-90) REVERT: B 1084 ASN cc_start: 0.8934 (p0) cc_final: 0.8539 (p0) REVERT: B 1145 GLN cc_start: 0.8821 (mt0) cc_final: 0.8435 (mt0) REVERT: D 148 GLU cc_start: 0.2663 (mm-30) cc_final: 0.2170 (mp0) REVERT: E 3 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7443 (t0) REVERT: E 46 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7507 (t0) REVERT: E 116 GLN cc_start: 0.7578 (tp-100) cc_final: 0.7086 (tp-100) REVERT: G 21 ASN cc_start: 0.8050 (m110) cc_final: 0.7769 (m-40) REVERT: G 164 MET cc_start: 0.2445 (ttp) cc_final: 0.1511 (tmm) REVERT: H 145 MET cc_start: 0.9074 (ptm) cc_final: 0.8838 (mtm) REVERT: I 82 GLU cc_start: 0.8235 (mm-30) cc_final: 0.8006 (mm-30) REVERT: L 35 ARG cc_start: 0.8567 (ttp80) cc_final: 0.8326 (ttt-90) outliers start: 49 outliers final: 28 residues processed: 430 average time/residue: 0.8387 time to fit residues: 421.9379 Evaluate side-chains 425 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 390 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ARG 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 637 MET 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 163 LEU 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 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 980 ILE 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 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 H residue 62 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 16 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 161 optimal weight: 0.1980 chunk 52 optimal weight: 0.6980 chunk 361 optimal weight: 2.9990 chunk 311 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 385 optimal weight: 50.0000 chunk 50 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 148 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS I 18 GLN I 32 ASN I 45 GLN I 56 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.102130 restraints weight = 38703.798| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.03 r_work: 0.2831 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 33698 Z= 0.150 Angle : 0.663 59.161 45858 Z= 0.364 Chirality : 0.044 0.467 5133 Planarity : 0.004 0.058 5659 Dihedral : 13.125 170.894 5164 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.21 % Allowed : 16.60 % Favored : 82.19 % 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: 0.28 (0.14), residues: 3864 helix: 1.21 (0.14), residues: 1351 sheet: -0.65 (0.19), residues: 621 loop : -0.16 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG E 187 TYR 0.021 0.001 TYR G 128 PHE 0.017 0.001 PHE A 592 TRP 0.013 0.001 TRP C 49 HIS 0.008 0.001 HIS B 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (33666) covalent geometry : angle 0.65340 / 0.36 (45813) hydrogen bonds : bond 0.03481 / 2.28 ( 1386) hydrogen bonds : angle 4.70250 / 3.36 ( 3902) metal coordination : bond 0.00581 / 0.44 ( 32) metal coordination : angle 3.70449 / 2.35 ( 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 432 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 390 time to evaluate : 1.373 Fit side-chains REVERT: A 291 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7053 (ttm170) REVERT: A 347 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7858 (mm-30) REVERT: A 540 ASP cc_start: 0.8598 (m-30) cc_final: 0.8342 (m-30) REVERT: A 1008 LYS cc_start: 0.8560 (mmtm) cc_final: 0.8027 (tttm) REVERT: A 1236 ASN cc_start: 0.7445 (m-40) cc_final: 0.7090 (m-40) REVERT: A 1247 PHE cc_start: 0.7034 (p90) cc_final: 0.6495 (p90) REVERT: A 1248 ASN cc_start: 0.7035 (t0) cc_final: 0.6679 (t160) REVERT: A 1451 MET cc_start: 0.9073 (mmm) cc_final: 0.8813 (mmm) REVERT: B 144 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6438 (mp) REVERT: B 166 GLU cc_start: 0.8279 (mp0) cc_final: 0.7864 (mp0) REVERT: B 362 LEU cc_start: 0.9006 (mt) cc_final: 0.8654 (mp) REVERT: B 375 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7065 (mmt) REVERT: B 515 ARG cc_start: 0.8179 (ttp-170) cc_final: 0.7577 (ttp80) REVERT: B 624 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: B 967 ARG cc_start: 0.7663 (ttp-110) cc_final: 0.7421 (ttt-90) REVERT: B 1084 ASN cc_start: 0.8932 (p0) cc_final: 0.8542 (p0) REVERT: B 1145 GLN cc_start: 0.8819 (mt0) cc_final: 0.8436 (mt0) REVERT: D 148 GLU cc_start: 0.2673 (mm-30) cc_final: 0.2169 (mp0) REVERT: E 3 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7461 (t0) REVERT: E 46 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7494 (t0) REVERT: E 116 GLN cc_start: 0.7577 (tp-100) cc_final: 0.7085 (tp-100) REVERT: G 21 ASN cc_start: 0.8052 (m110) cc_final: 0.7769 (m-40) REVERT: G 164 MET cc_start: 0.2458 (ttp) cc_final: 0.1508 (tmm) REVERT: H 145 MET cc_start: 0.9085 (ptm) cc_final: 0.8852 (mtm) REVERT: J 66 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6663 (mm-30) REVERT: L 35 ARG cc_start: 0.8577 (ttp80) cc_final: 0.8331 (ttt-90) outliers start: 42 outliers final: 28 residues processed: 412 average time/residue: 0.8423 time to fit residues: 406.6096 Evaluate side-chains 424 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 389 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ARG 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 637 MET 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 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 980 ILE 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 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 76 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 16 ILE 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: 0.2980 chunk 246 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 230 optimal weight: 3.9990 chunk 340 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 282 optimal weight: 30.0000 chunk 171 optimal weight: 0.4980 chunk 200 optimal weight: 4.9990 chunk 260 optimal weight: 0.0770 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS I 32 ASN I 45 GLN I 56 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.102072 restraints weight = 38489.911| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.03 r_work: 0.2823 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 33698 Z= 0.149 Angle : 0.663 59.200 45858 Z= 0.364 Chirality : 0.044 0.460 5133 Planarity : 0.004 0.058 5659 Dihedral : 13.125 170.894 5164 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.04 % Allowed : 16.80 % Favored : 82.16 % 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: 0.28 (0.14), residues: 3864 helix: 1.21 (0.14), residues: 1351 sheet: -0.65 (0.19), residues: 621 loop : -0.16 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG E 187 TYR 0.021 0.001 TYR G 128 PHE 0.017 0.001 PHE A 592 TRP 0.013 0.001 TRP C 49 HIS 0.008 0.001 HIS B 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (33666) covalent geometry : angle 0.65332 / 0.36 (45813) hydrogen bonds : bond 0.03481 / 2.28 ( 1386) hydrogen bonds : angle 4.70233 / 3.36 ( 3902) metal coordination : bond 0.00581 / 0.44 ( 32) metal coordination : angle 3.70443 / 2.35 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13198.05 seconds wall clock time: 225 minutes 19.20 seconds (13519.20 seconds total)