Starting phenix.real_space_refine on Tue Sep 15 20:54:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gml_0038/09_2026/6gml_0038_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gml_0038/09_2026/6gml_0038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6gml_0038/09_2026/6gml_0038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gml_0038/09_2026/6gml_0038.map" model { file = "/net/cci-nas-00/data/ceres_data/6gml_0038/09_2026/6gml_0038_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gml_0038/09_2026/6gml_0038_neut.cif" } resolution = 3.2 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= 0.002 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 9 6.06 5 P 98 5.49 5 Mg 1 5.21 5 S 246 5.16 5 C 27762 2.51 5 N 7991 2.21 5 O 8720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.05s 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: 44827 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 11142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1407, 11142 Classifications: {'peptide': 1407} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1337} Chain breaks: 5 Chain: "B" Number of atoms: 8928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8928 Classifications: {'peptide': 1116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 53, 'TRANS': 1062} Chain breaks: 6 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2072 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 242} 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: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 76} 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: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 950 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} 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: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 389 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "N" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 730 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain breaks: 1 Chain: "P" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 361 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna2p': 5, 'rna3p': 11} Chain: "T" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 933 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "U" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1410 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 11, 'TRANS': 171} Chain: "V" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 1932 Classifications: {'peptide': 483} Incomplete info: {'backbone_only': 463} Link IDs: {'PTRANS': 17, 'TRANS': 465} Chain breaks: 7 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1993 Unresolved non-hydrogen angles: 2888 Unresolved non-hydrogen dihedrals: 1241 Unresolved non-hydrogen chiralities: 606 Planarities with less than four sites: {'UNK:plan-1': 38, 'GLN:plan1': 21, 'PHE:plan': 26, 'ASP:plan': 24, 'HIS:plan': 13, 'ARG:plan': 25, 'GLU:plan': 36, 'TYR:plan': 9, 'TRP:plan': 3, 'ASN:plan1': 8} Unresolved non-hydrogen planarities: 881 Chain: "W" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 3858 Classifications: {'peptide': 538} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 516} Chain breaks: 2 Unresolved non-hydrogen bonds: 392 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'UNK:plan-1': 41, 'GLN:plan1': 7, 'ASN:plan1': 3, 'GLU:plan': 9, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 4, 'ASP:plan': 5, 'ARG:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 224 Chain: "X" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "Y" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 3770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3770 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 16, 'TRANS': 453} Chain breaks: 7 Chain: "D" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 998 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1305 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" 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 768 SG CYS A 111 93.380 72.431 137.194 1.00 52.15 S ATOM 796 SG CYS A 114 93.723 72.406 141.521 1.00 60.58 S ATOM 464 SG CYS A 71 47.340 71.891 125.479 1.00 41.25 S ATOM 486 SG CYS A 74 47.060 75.962 124.614 1.00 35.32 S ATOM 533 SG CYS A 81 48.143 73.806 121.757 1.00 35.83 S ATOM 19639 SG CYS B1119 58.135 85.562 129.404 1.00 32.24 S ATOM 19661 SG CYS B1122 61.242 83.877 130.290 1.00 35.98 S ATOM 19776 SG CYS B1137 57.759 82.371 130.958 1.00 48.78 S ATOM 20764 SG CYS C 88 11.221 76.621 66.450 1.00 27.25 S ATOM 20777 SG CYS C 90 11.932 73.821 69.028 1.00 37.75 S ATOM 20812 SG CYS C 94 11.056 73.106 65.533 1.00 23.11 S ATOM 20834 SG CYS C 97 14.614 73.590 65.899 1.00 16.65 S ATOM 25776 SG CYS I 17 125.353 34.343 92.308 1.00 39.89 S ATOM 25800 SG CYS I 20 122.701 34.499 94.757 1.00 41.99 S ATOM 25961 SG CYS I 39 124.020 37.747 95.721 1.00 38.99 S ATOM 25986 SG CYS I 42 126.257 34.422 95.826 1.00 43.23 S ATOM 26338 SG CYS I 86 113.852 47.359 51.643 1.00 32.07 S ATOM 26362 SG CYS I 89 112.826 44.359 49.722 1.00 31.64 S ATOM 26601 SG CYS I 119 111.302 43.030 52.749 1.00 38.63 S ATOM 26712 SG CYS J 7 42.310 68.307 52.595 1.00 28.01 S ATOM 26736 SG CYS J 10 41.342 72.018 49.781 1.00 23.57 S ATOM 27000 SG CYS J 44 44.557 70.683 50.305 1.00 23.69 S ATOM 27006 SG CYS J 45 41.593 68.124 48.967 1.00 21.59 S ATOM 28187 SG CYS L 22 33.873 32.997 80.209 1.00 35.66 S ATOM 28304 SG CYS L 36 31.961 33.302 83.247 1.00 37.97 S ATOM 37952 SG CYS Y 16 70.632 21.433 150.340 1.00 81.24 S ATOM 37974 SG CYS Y 19 74.637 21.329 148.716 1.00 84.47 S ATOM 38086 SG CYS Y 33 73.062 17.922 148.915 1.00 73.71 S Time building chain proxies: 8.76, per 1000 atoms: 0.20 Number of scatterers: 44827 At special positions: 0 Unit cell: (155.918, 186.61, 185.383, 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 9 29.99 S 246 16.00 P 98 15.00 Mg 1 11.99 O 8720 8.00 N 7991 7.00 C 27762 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: 3.31 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 74 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1119 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1122 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1137 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb=" ZN I 200 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 39 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " 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 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 16 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 33 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " Number of angles added : 21 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9804 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 58 sheets defined 43.5% alpha, 15.2% beta 44 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 5.75 Creating SS restraints... Processing helix chain 'A' and resid 27 through 33 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.601A pdb=" N LEU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 removed outlier: 3.695A pdb=" N ASN A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 319 removed outlier: 4.499A pdb=" N LYS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 4.326A pdb=" N GLY A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.714A pdb=" N ASP A 437 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 434 through 438' Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 564 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 659 Processing helix chain 'A' and resid 662 through 684 removed outlier: 4.070A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 693 removed outlier: 3.844A pdb=" N ILE A 693 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 removed outlier: 3.625A pdb=" N ASN A 722 " --> pdb=" O GLU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 757 Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.638A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.556A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 868 removed outlier: 4.105A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 removed outlier: 3.531A pdb=" N ASP A 894 " --> pdb=" O TYR A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.891A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 946 through 970 Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1078 Processing helix chain 'A' and resid 1086 through 1102 Proline residue: A1098 - end of helix removed outlier: 4.156A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 3.835A pdb=" N TRP A1192 " --> pdb=" O ASP A1189 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A1194 " --> pdb=" O GLU A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.785A pdb=" N MET A1221 " --> pdb=" O ASP A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.533A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1294 removed outlier: 3.994A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 removed outlier: 3.853A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1388 Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.750A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1435 through 1445 removed outlier: 3.648A pdb=" N LEU A1439 " --> pdb=" O THR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1460 Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.323A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 5.270A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 306 removed outlier: 3.742A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 335 through 346 Processing helix chain 'B' and resid 348 through 352 removed outlier: 3.687A pdb=" N VAL B 351 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 378 Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.934A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP B 424 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 450 removed outlier: 4.196A pdb=" N GLY B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 583 through 592 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.656A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 removed outlier: 3.605A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.646A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.502A pdb=" N GLN B 683 " --> pdb=" O PRO B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.513A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 762 through 766 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 968 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.968A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.862A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1059 Processing helix chain 'B' and resid 1077 through 1081 removed outlier: 3.645A pdb=" N ARG B1080 " --> pdb=" O GLY B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 27 through 40 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.709A pdb=" N ASN C 177 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.925A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.565A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 83 through 97 removed outlier: 4.422A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 removed outlier: 3.615A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 removed outlier: 3.811A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 removed outlier: 3.525A pdb=" N GLY F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.948A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 68 removed outlier: 4.201A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.826A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 removed outlier: 3.549A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.965A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 4.132A 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 9 removed outlier: 3.780A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 5.811A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 114 removed outlier: 3.726A pdb=" N THR K 92 " --> pdb=" O THR K 88 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 18 Processing helix chain 'U' and resid 34 through 42 Processing helix chain 'U' and resid 49 through 60 Processing helix chain 'U' and resid 64 through 71 removed outlier: 3.789A pdb=" N MET U 71 " --> pdb=" O THR U 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 84 removed outlier: 3.558A pdb=" N LEU U 75 " --> pdb=" O MET U 71 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU U 84 " --> pdb=" O GLN U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 98 Processing helix chain 'U' and resid 114 through 131 removed outlier: 3.550A pdb=" N GLN U 118 " --> pdb=" O ASN U 114 " (cutoff:3.500A) Processing helix chain 'U' and resid 138 through 143 removed outlier: 3.836A pdb=" N GLN U 142 " --> pdb=" O LEU U 139 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 154 removed outlier: 3.543A pdb=" N GLY U 154 " --> pdb=" O THR U 150 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 187 removed outlier: 4.080A pdb=" N THR U 173 " --> pdb=" O PRO U 169 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 20 removed outlier: 3.614A pdb=" N UNK V 12 " --> pdb=" O UNK V 8 " (cutoff:3.500A) Processing helix chain 'V' and resid 26 through 35 removed outlier: 4.032A pdb=" N UNK V 35 " --> pdb=" O UNK V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 41 through 52 Proline residue: V 49 - end of helix Processing helix chain 'V' and resid 57 through 80 removed outlier: 3.683A pdb=" N PHE V 61 " --> pdb=" O PRO V 57 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LYS V 72 " --> pdb=" O GLU V 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 103 Processing helix chain 'V' and resid 110 through 119 removed outlier: 4.168A pdb=" N HIS V 119 " --> pdb=" O CYS V 115 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 133 removed outlier: 3.528A pdb=" N ALA V 133 " --> pdb=" O LYS V 129 " (cutoff:3.500A) Processing helix chain 'V' and resid 138 through 143 Processing helix chain 'V' and resid 155 through 176 removed outlier: 4.162A pdb=" N SER V 162 " --> pdb=" O GLY V 158 " (cutoff:3.500A) Proline residue: V 163 - end of helix Processing helix chain 'V' and resid 200 through 207 Processing helix chain 'V' and resid 211 through 230 Processing helix chain 'V' and resid 233 through 243 removed outlier: 3.632A pdb=" N LEU V 237 " --> pdb=" O HIS V 233 " (cutoff:3.500A) Processing helix chain 'V' and resid 260 through 273 removed outlier: 4.630A pdb=" N CYS V 269 " --> pdb=" O CYS V 265 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE V 270 " --> pdb=" O LEU V 266 " (cutoff:3.500A) Processing helix chain 'V' and resid 277 through 289 removed outlier: 3.648A pdb=" N GLY V 289 " --> pdb=" O GLY V 285 " (cutoff:3.500A) Processing helix chain 'V' and resid 295 through 306 removed outlier: 3.648A pdb=" N CYS V 306 " --> pdb=" O SER V 302 " (cutoff:3.500A) Processing helix chain 'V' and resid 307 through 329 Processing helix chain 'V' and resid 339 through 352 Processing helix chain 'V' and resid 367 through 387 removed outlier: 3.910A pdb=" N THR V 371 " --> pdb=" O VAL V 367 " (cutoff:3.500A) Proline residue: V 375 - end of helix Processing helix chain 'V' and resid 409 through 417 Processing helix chain 'V' and resid 421 through 429 Processing helix chain 'V' and resid 439 through 453 Proline residue: V 446 - end of helix Processing helix chain 'V' and resid 459 through 475 Processing helix chain 'V' and resid 476 through 489 Processing helix chain 'V' and resid 495 through 508 Processing helix chain 'V' and resid 515 through 525 removed outlier: 3.788A pdb=" N GLN V 524 " --> pdb=" O LEU V 520 " (cutoff:3.500A) Processing helix chain 'V' and resid 532 through 547 removed outlier: 3.542A pdb=" N ALA V 536 " --> pdb=" O GLN V 532 " (cutoff:3.500A) Processing helix chain 'W' and resid 57 through 60 removed outlier: 3.951A pdb=" N UNK W 60 " --> pdb=" O UNK W 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 57 through 60' Processing helix chain 'W' and resid 61 through 71 removed outlier: 3.576A pdb=" N UNK W 65 " --> pdb=" O UNK W 61 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N UNK W 71 " --> pdb=" O UNK W 67 " (cutoff:3.500A) Processing helix chain 'W' and resid 76 through 84 Processing helix chain 'W' and resid 90 through 105 removed outlier: 4.036A pdb=" N LEU W 96 " --> pdb=" O GLN W 92 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU W 99 " --> pdb=" O ASN W 95 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP W 100 " --> pdb=" O LEU W 96 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR W 104 " --> pdb=" O TRP W 100 " (cutoff:3.500A) Processing helix chain 'W' and resid 110 through 127 Processing helix chain 'W' and resid 132 through 140 removed outlier: 3.980A pdb=" N GLY W 140 " --> pdb=" O PHE W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 143 through 152 removed outlier: 3.548A pdb=" N GLU W 147 " --> pdb=" O PRO W 143 " (cutoff:3.500A) Processing helix chain 'W' and resid 155 through 164 removed outlier: 3.798A pdb=" N GLU W 164 " --> pdb=" O TYR W 160 " (cutoff:3.500A) Processing helix chain 'W' and resid 168 through 182 Processing helix chain 'W' and resid 197 through 216 removed outlier: 3.790A pdb=" N ARG W 203 " --> pdb=" O GLU W 199 " (cutoff:3.500A) Processing helix chain 'W' and resid 218 through 223 removed outlier: 4.063A pdb=" N LYS W 222 " --> pdb=" O GLU W 218 " (cutoff:3.500A) Processing helix chain 'W' and resid 223 through 232 removed outlier: 4.942A pdb=" N MET W 230 " --> pdb=" O GLU W 226 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL W 231 " --> pdb=" O PHE W 227 " (cutoff:3.500A) Processing helix chain 'W' and resid 234 through 249 Processing helix chain 'W' and resid 254 through 273 removed outlier: 4.357A pdb=" N VAL W 258 " --> pdb=" O GLY W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 276 through 284 Processing helix chain 'W' and resid 285 through 288 Processing helix chain 'W' and resid 289 through 303 removed outlier: 3.600A pdb=" N CYS W 293 " --> pdb=" O TYR W 289 " (cutoff:3.500A) Processing helix chain 'W' and resid 306 through 317 removed outlier: 3.617A pdb=" N MET W 316 " --> pdb=" O VAL W 312 " (cutoff:3.500A) Processing helix chain 'W' and resid 324 through 328 Processing helix chain 'W' and resid 330 through 343 removed outlier: 3.805A pdb=" N LYS W 343 " --> pdb=" O GLN W 339 " (cutoff:3.500A) Processing helix chain 'W' and resid 352 through 366 removed outlier: 3.980A pdb=" N VAL W 366 " --> pdb=" O TYR W 362 " (cutoff:3.500A) Processing helix chain 'W' and resid 382 through 400 removed outlier: 4.177A pdb=" N GLU W 400 " --> pdb=" O LEU W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 401 through 410 Processing helix chain 'W' and resid 410 through 418 Processing helix chain 'W' and resid 420 through 436 Processing helix chain 'W' and resid 449 through 462 Processing helix chain 'W' and resid 465 through 479 Processing helix chain 'W' and resid 485 through 506 Processing helix chain 'W' and resid 509 through 522 Processing helix chain 'W' and resid 526 through 539 removed outlier: 3.642A pdb=" N ILE W 530 " --> pdb=" O ASP W 526 " (cutoff:3.500A) Processing helix chain 'W' and resid 546 through 559 Proline residue: W 555 - end of helix Processing helix chain 'W' and resid 562 through 566 removed outlier: 3.601A pdb=" N THR W 565 " --> pdb=" O ILE W 562 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE W 566 " --> pdb=" O ALA W 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 562 through 566' Processing helix chain 'W' and resid 575 through 586 Processing helix chain 'X' and resid 4 through 18 Processing helix chain 'Y' and resid 25 through 32 Processing helix chain 'Y' and resid 36 through 41 Processing helix chain 'Y' and resid 45 through 52 removed outlier: 3.643A pdb=" N VAL Y 49 " --> pdb=" O ASN Y 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 68 Processing helix chain 'Y' and resid 69 through 75 Processing helix chain 'Y' and resid 94 through 104 Processing helix chain 'Z' and resid 189 through 203 Processing helix chain 'Z' and resid 231 through 239 removed outlier: 3.653A pdb=" N VAL Z 235 " --> pdb=" O LYS Z 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 245 through 249 removed outlier: 3.563A pdb=" N TYR Z 249 " --> pdb=" O ARG Z 246 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 260 removed outlier: 3.718A pdb=" N MET Z 260 " --> pdb=" O ILE Z 257 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 349 removed outlier: 3.547A pdb=" N GLY Z 349 " --> pdb=" O ILE Z 345 " (cutoff:3.500A) Processing helix chain 'Z' and resid 389 through 396 Processing helix chain 'Z' and resid 630 through 633 removed outlier: 4.186A pdb=" N GLY Z 633 " --> pdb=" O VAL Z 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 630 through 633' Processing helix chain 'D' and resid 16 through 20 removed outlier: 3.516A pdb=" N GLN D 19 " --> pdb=" O ASP D 16 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU D 20 " --> pdb=" O ALA D 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 16 through 20' Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.627A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.931A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' 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 86 through 88 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.554A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 362 through 369 removed outlier: 8.134A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.723A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.550A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.224A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE B 965 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE B 779 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE B 967 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA B 781 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL B 794 " --> pdb=" O CYS B 945 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE B 947 " --> pdb=" O VAL B 794 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.224A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB4, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.954A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB6, first strand: chain 'A' and resid 1139 through 1140 removed outlier: 3.706A pdb=" N THR A1140 " --> pdb=" O THR A1358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1243 through 1246 removed outlier: 3.999A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1308 through 1310 Processing sheet with id=AB9, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC1, first strand: chain 'A' and resid 1472 through 1475 Processing sheet with id=AC2, first strand: chain 'B' and resid 65 through 67 removed outlier: 5.736A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.541A pdb=" N SER B 106 " --> pdb=" O HIS B 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.349A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 205 through 208 removed outlier: 3.795A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER B 223 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC8, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC9, first strand: chain 'B' and resid 551 through 552 removed outlier: 7.177A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.683A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.683A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD4, first strand: chain 'B' and resid 827 through 829 removed outlier: 7.344A pdb=" N GLN B 838 " --> pdb=" O ASP B 891 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.526A pdb=" N ILE B 866 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AD7, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD8, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.827A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.333A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 113 through 115 Processing sheet with id=AE2, first strand: chain 'E' and resid 102 through 105 Processing sheet with id=AE3, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE4, first strand: chain 'H' and resid 139 through 142 removed outlier: 3.847A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AE6, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE7, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE8, first strand: chain 'U' and resid 164 through 165 Processing sheet with id=AE9, first strand: chain 'Y' and resid 22 through 24 Processing sheet with id=AF1, first strand: chain 'Y' and resid 83 through 90 removed outlier: 7.117A pdb=" N GLY Y 59 " --> pdb=" O VAL Y 87 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL Y 89 " --> pdb=" O PHE Y 57 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE Y 57 " --> pdb=" O VAL Y 89 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE Y 60 " --> pdb=" O ALA Z 217 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER Z 214 " --> pdb=" O GLU Z 228 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN Z 253 " --> pdb=" O THR Z 181 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Z' and resid 278 through 280 removed outlier: 6.756A pdb=" N SER Z 304 " --> pdb=" O ASP Z 294 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL Z 296 " --> pdb=" O THR Z 302 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N THR Z 302 " --> pdb=" O VAL Z 296 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 352 through 355 Processing sheet with id=AF4, first strand: chain 'Z' and resid 453 through 454 Processing sheet with id=AF5, first strand: chain 'Z' and resid 510 through 513 removed outlier: 7.270A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.493A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR Z 546 " --> pdb=" O LEU Z 542 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR Z 576 " --> pdb=" O GLN Z 541 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 586 through 587 Processing sheet with id=AF8, first strand: chain 'Z' and resid 635 through 639 removed outlier: 6.656A pdb=" N PHE Z 621 " --> pdb=" O LEU Z 617 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU Z 617 " --> pdb=" O PHE Z 621 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 742 through 746 removed outlier: 6.953A pdb=" N THR Z 731 " --> pdb=" O ALA Z 727 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA Z 727 " --> pdb=" O THR Z 731 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG Z 733 " --> pdb=" O LYS Z 725 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.754A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.754A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.525A pdb=" N GLY G 169 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY G 161 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 118 through 120 1990 hydrogen bonds defined for protein. 5631 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 110 hydrogen bonds 220 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 14.06 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9130 1.33 - 1.45: 10582 1.45 - 1.57: 25514 1.57 - 1.69: 192 1.69 - 1.81: 388 Bond restraints: 45806 Sorted by residual: bond pdb=" N9 DG T 26 " pdb=" C4 DG T 26 " ideal model delta sigma weight residual 1.375 1.407 -0.032 8.00e-03 1.56e+04 1.61e+01 bond pdb=" CA PRO U 26 " pdb=" C PRO U 26 " ideal model delta sigma weight residual 1.517 1.493 0.024 6.70e-03 2.23e+04 1.30e+01 bond pdb=" N LEU W 523 " pdb=" CA LEU W 523 " ideal model delta sigma weight residual 1.462 1.507 -0.046 1.31e-02 5.83e+03 1.22e+01 bond pdb=" C5' DA N 36 " pdb=" C4' DA N 36 " ideal model delta sigma weight residual 1.512 1.535 -0.023 7.00e-03 2.04e+04 1.12e+01 bond pdb=" C5' DC N 13 " pdb=" C4' DC N 13 " ideal model delta sigma weight residual 1.512 1.533 -0.021 7.00e-03 2.04e+04 9.31e+00 ... (remaining 45801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 60708 2.73 - 5.45: 1236 5.45 - 8.18: 165 8.18 - 10.91: 41 10.91 - 13.63: 6 Bond angle restraints: 62156 Sorted by residual: angle pdb=" C ILE W 418 " pdb=" CA ILE W 418 " pdb=" CB ILE W 418 " ideal model delta sigma weight residual 111.29 120.82 -9.53 1.64e+00 3.72e-01 3.38e+01 angle pdb=" O4' DA T 35 " pdb=" C4' DA T 35 " pdb=" C3' DA T 35 " ideal model delta sigma weight residual 106.00 102.56 3.44 6.00e-01 2.78e+00 3.28e+01 angle pdb=" N ILE W 418 " pdb=" CA ILE W 418 " pdb=" CB ILE W 418 " ideal model delta sigma weight residual 111.23 102.27 8.96 1.65e+00 3.67e-01 2.95e+01 angle pdb=" C PRO K 79 " pdb=" N ASP K 80 " pdb=" CA ASP K 80 " ideal model delta sigma weight residual 125.66 135.44 -9.78 1.85e+00 2.92e-01 2.79e+01 angle pdb=" O5' G P 37 " pdb=" C5' G P 37 " pdb=" C4' G P 37 " ideal model delta sigma weight residual 109.40 113.57 -4.17 8.00e-01 1.56e+00 2.72e+01 ... (remaining 62151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.78: 26290 32.78 - 65.55: 760 65.55 - 98.33: 52 98.33 - 131.10: 1 131.10 - 163.88: 2 Dihedral angle restraints: 27105 sinusoidal: 11515 harmonic: 15590 Sorted by residual: dihedral pdb=" CA HIS A1108 " pdb=" C HIS A1108 " pdb=" N TYR A1109 " pdb=" CA TYR A1109 " ideal model delta harmonic sigma weight residual 180.00 129.46 50.54 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA GLU B 629 " pdb=" C GLU B 629 " pdb=" N LYS B 630 " pdb=" CA LYS B 630 " ideal model delta harmonic sigma weight residual -180.00 -133.36 -46.64 0 5.00e+00 4.00e-02 8.70e+01 dihedral pdb=" CA LYS A 910 " pdb=" C LYS A 910 " pdb=" N PRO A 911 " pdb=" CA PRO A 911 " ideal model delta harmonic sigma weight residual 180.00 141.45 38.55 0 5.00e+00 4.00e-02 5.95e+01 ... (remaining 27102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 5824 0.083 - 0.167: 894 0.167 - 0.250: 52 0.250 - 0.333: 8 0.333 - 0.417: 6 Chirality restraints: 6784 Sorted by residual: chirality pdb=" CG LEU A 405 " pdb=" CB LEU A 405 " pdb=" CD1 LEU A 405 " pdb=" CD2 LEU A 405 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CB ILE B 621 " pdb=" CA ILE B 621 " pdb=" CG1 ILE B 621 " pdb=" CG2 ILE B 621 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CB ILE A 419 " pdb=" CA ILE A 419 " pdb=" CG1 ILE A 419 " pdb=" CG2 ILE A 419 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 6781 not shown) Planarity restraints: 7864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN W 401 " 0.025 2.00e-02 2.50e+03 4.89e-02 2.39e+01 pdb=" C ASN W 401 " -0.085 2.00e-02 2.50e+03 pdb=" O ASN W 401 " 0.032 2.00e-02 2.50e+03 pdb=" N ALA W 404 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER U 182 " 0.025 2.00e-02 2.50e+03 4.79e-02 2.29e+01 pdb=" C SER U 182 " -0.083 2.00e-02 2.50e+03 pdb=" O SER U 182 " 0.031 2.00e-02 2.50e+03 pdb=" N THR U 183 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN W 444 " -0.024 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" C GLN W 444 " 0.081 2.00e-02 2.50e+03 pdb=" O GLN W 444 " -0.030 2.00e-02 2.50e+03 pdb=" N THR W 445 " -0.027 2.00e-02 2.50e+03 ... (remaining 7861 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 455 2.62 - 3.19: 37857 3.19 - 3.76: 70432 3.76 - 4.33: 96533 4.33 - 4.90: 156715 Nonbonded interactions: 361992 Sorted by model distance: nonbonded pdb=" NE2 GLN W 444 " pdb=" OE2 GLU W 488 " model vdw 2.054 3.120 nonbonded pdb=" OD2 ASP Y 58 " pdb=" NZ LYS Z 268 " model vdw 2.057 3.120 nonbonded pdb=" OD2 ASP B 851 " pdb=" OH TYR L 17 " model vdw 2.084 3.040 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2001 " model vdw 2.095 2.170 nonbonded pdb=" NZ LYS A 149 " pdb=" OP2 DG T 14 " model vdw 2.108 3.120 ... (remaining 361987 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 50.990 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.100 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 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 : 0.009 0.401 45835 Z= 0.398 Angle : 1.049 53.483 62177 Z= 0.570 Chirality : 0.059 0.417 6784 Planarity : 0.007 0.104 7864 Dihedral : 13.653 163.877 17301 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.91 % Favored : 94.06 % Rotamer: Outliers : 0.43 % Allowed : 4.74 % Favored : 94.83 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.11 % 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: -3.52 (0.09), residues: 5485 helix: -2.34 (0.08), residues: 2176 sheet: -2.09 (0.18), residues: 664 loop : -2.33 (0.11), residues: 2645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 924 TYR 0.049 0.003 TYR B1048 PHE 0.051 0.004 PHE A 482 TRP 0.061 0.004 TRP B 573 HIS 0.017 0.003 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00757 / 0.35 (45806) covalent geometry : angle 0.98424 / 0.57 (62156) hydrogen bonds : bond 0.14028 / 9.32 ( 2067) hydrogen bonds : angle 7.06593 / 4.95 ( 5851) metal coordination : bond 0.21704 / 14.66 ( 29) metal coordination : angle 19.80927 / 14.69 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 956 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 968 ASN cc_start: 0.6432 (t0) cc_final: 0.5821 (t0) REVERT: E 49 SER cc_start: 0.6578 (m) cc_final: 0.6094 (p) REVERT: Z 222 LYS cc_start: 0.4238 (mttp) cc_final: 0.3763 (pttp) outliers start: 19 outliers final: 4 residues processed: 969 average time/residue: 0.2726 time to fit residues: 425.3454 Evaluate side-chains 431 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 427 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain W residue 330 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 394 optimal weight: 50.0000 chunk 430 optimal weight: 40.0000 chunk 41 optimal weight: 0.9990 chunk 265 optimal weight: 3.9990 chunk 523 optimal weight: 30.0000 chunk 497 optimal weight: 3.9990 chunk 414 optimal weight: 50.0000 chunk 310 optimal weight: 9.9990 chunk 488 optimal weight: 20.0000 chunk 366 optimal weight: 10.0000 chunk 223 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN A 272 ASN A 293 ASN ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 ASN A 403 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN A 576 GLN A 609 HIS A 654 HIS A 662 HIS A 740 GLN A 780 ASN A 809 HIS ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 ASN A 989 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN A1093 GLN A1129 ASN A1163 HIS A1244 ASN A1248 ASN A1299 GLN A1310 HIS A1457 ASN B 111 ASN B 486 ASN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 HIS B 639 HIS B 650 ASN B 699 HIS B 741 HIS B 749 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 HIS B1003 ASN B1021 HIS ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1133 HIS C 55 ASN C 232 ASN E 43 GLN E 107 GLN E 132 GLN E 168 ASN ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN I 22 ASN I 41 ASN I 91 HIS I 100 HIS J 52 HIS K 2 ASN U 80 GLN U 147 ASN U 164 GLN ** W 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 352 HIS W 394 HIS W 444 GLN W 451 HIS W 502 HIS Y 12 HIS Y 41 GLN Z 220 HIS ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.122349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.078648 restraints weight = 117195.771| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.94 r_work: 0.3069 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.168 45835 Z= 0.280 Angle : 0.787 19.879 62177 Z= 0.406 Chirality : 0.049 0.316 6784 Planarity : 0.006 0.086 7864 Dihedral : 14.870 167.609 7245 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.95 % Rotamer: Outliers : 3.16 % Allowed : 9.75 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.04 % 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: -1.94 (0.10), residues: 5485 helix: -0.55 (0.10), residues: 2226 sheet: -1.71 (0.18), residues: 709 loop : -1.77 (0.12), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 24 TYR 0.033 0.002 TYR B1048 PHE 0.034 0.002 PHE Z 200 TRP 0.026 0.002 TRP A 988 HIS 0.013 0.002 HIS Z 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.28 (45806) covalent geometry : angle 0.77334 / 0.41 (62156) hydrogen bonds : bond 0.04463 / 2.98 ( 2067) hydrogen bonds : angle 5.40537 / 3.77 ( 5851) metal coordination : bond 0.01682 / 1.10 ( 29) metal coordination : angle 8.03073 / 5.40 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 434 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.7673 (ptt) cc_final: 0.7427 (ptp) REVERT: A 118 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8414 (mt) REVERT: A 248 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8378 (mmm) REVERT: A 501 MET cc_start: 0.9394 (mtp) cc_final: 0.9183 (ttm) REVERT: A 535 MET cc_start: 0.9199 (mmt) cc_final: 0.8686 (mmt) REVERT: A 715 GLU cc_start: 0.8747 (pp20) cc_final: 0.8336 (pp20) REVERT: A 1119 LEU cc_start: 0.8830 (mt) cc_final: 0.8619 (mm) REVERT: A 1361 ASP cc_start: 0.8522 (t0) cc_final: 0.8155 (t0) REVERT: B 199 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8755 (pttt) REVERT: B 315 ASN cc_start: 0.9162 (m-40) cc_final: 0.8954 (m-40) REVERT: E 52 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8315 (ptp90) REVERT: H 20 LYS cc_start: 0.9068 (tttm) cc_final: 0.8836 (tptp) REVERT: H 107 GLU cc_start: 0.8388 (pm20) cc_final: 0.8183 (pm20) REVERT: I 23 MET cc_start: 0.8192 (ttp) cc_final: 0.7979 (ttm) REVERT: K 102 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8371 (tm-30) REVERT: L 27 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8151 (mm-30) REVERT: L 44 MET cc_start: 0.8843 (mmt) cc_final: 0.8396 (mmt) REVERT: U 71 MET cc_start: 0.7546 (pmm) cc_final: 0.7030 (pmm) REVERT: U 98 LYS cc_start: 0.8599 (pttt) cc_final: 0.8368 (mttt) REVERT: W 245 MET cc_start: 0.9007 (mmm) cc_final: 0.8714 (mtt) REVERT: W 457 GLU cc_start: 0.9000 (tp30) cc_final: 0.8605 (tp30) REVERT: W 566 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.7021 (tp) REVERT: Y 42 MET cc_start: 0.0858 (mpp) cc_final: 0.0589 (mpp) REVERT: Z 481 ILE cc_start: 0.5031 (OUTLIER) cc_final: 0.4794 (mp) REVERT: D 76 ASN cc_start: 0.6103 (t0) cc_final: 0.5776 (t0) REVERT: G 53 ASN cc_start: 0.8444 (p0) cc_final: 0.8085 (p0) REVERT: G 63 ARG cc_start: 0.8166 (mmm160) cc_final: 0.7084 (mmm-85) outliers start: 140 outliers final: 65 residues processed: 540 average time/residue: 0.2414 time to fit residues: 220.9645 Evaluate side-chains 430 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 359 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 924 TYR Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1192 TRP Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain U residue 119 ASP Chi-restraints excluded: chain U residue 173 THR Chi-restraints excluded: chain W residue 189 THR Chi-restraints excluded: chain W residue 232 CYS Chi-restraints excluded: chain W residue 271 GLU Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 413 THR Chi-restraints excluded: chain W residue 469 VAL Chi-restraints excluded: chain W residue 470 LEU Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 559 ASN Chi-restraints excluded: chain W residue 562 ILE Chi-restraints excluded: chain W residue 566 ILE Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain G residue 6 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 291 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 469 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 452 optimal weight: 10.0000 chunk 170 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 343 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 HIS ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 HIS ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN K 84 GLN U 147 ASN U 188 GLN W 253 GLN Z 220 HIS ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 737 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.123334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.079960 restraints weight = 116249.215| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.91 r_work: 0.3104 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 45835 Z= 0.140 Angle : 0.629 17.490 62177 Z= 0.322 Chirality : 0.045 0.272 6784 Planarity : 0.004 0.072 7864 Dihedral : 14.685 168.923 7245 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.31 % Rotamer: Outliers : 2.08 % Allowed : 11.22 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.11), residues: 5485 helix: 0.30 (0.11), residues: 2221 sheet: -1.51 (0.18), residues: 731 loop : -1.54 (0.12), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 193 TYR 0.021 0.002 TYR B 388 PHE 0.026 0.002 PHE Z 200 TRP 0.017 0.001 TRP A 988 HIS 0.010 0.001 HIS A 804 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (45806) covalent geometry : angle 0.61806 / 0.32 (62156) hydrogen bonds : bond 0.03748 / 2.52 ( 2067) hydrogen bonds : angle 4.95998 / 3.46 ( 5851) metal coordination : bond 0.00646 / 0.45 ( 29) metal coordination : angle 6.25132 / 4.01 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 382 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.7649 (ptt) cc_final: 0.7420 (ptp) REVERT: A 118 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8486 (mt) REVERT: A 238 MET cc_start: 0.7029 (ttm) cc_final: 0.6828 (mtt) REVERT: A 248 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8383 (mmm) REVERT: A 329 MET cc_start: 0.7941 (ptp) cc_final: 0.7471 (ttp) REVERT: A 469 MET cc_start: 0.9140 (ttt) cc_final: 0.8672 (ttm) REVERT: A 501 MET cc_start: 0.9394 (mtp) cc_final: 0.8897 (mtp) REVERT: A 715 GLU cc_start: 0.8757 (pp20) cc_final: 0.8315 (pp20) REVERT: A 1102 MET cc_start: 0.7596 (ptp) cc_final: 0.7371 (ptp) REVERT: A 1361 ASP cc_start: 0.8478 (t0) cc_final: 0.7985 (t70) REVERT: B 108 MET cc_start: 0.9135 (ttp) cc_final: 0.8732 (ptm) REVERT: B 1151 MET cc_start: 0.8961 (ptt) cc_final: 0.8337 (ptt) REVERT: C 15 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8284 (p) REVERT: C 215 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8542 (mt-10) REVERT: E 65 ASN cc_start: 0.8960 (p0) cc_final: 0.8151 (m-40) REVERT: H 20 LYS cc_start: 0.9033 (tttm) cc_final: 0.8824 (tptp) REVERT: H 42 ASP cc_start: 0.8820 (m-30) cc_final: 0.8409 (m-30) REVERT: H 107 GLU cc_start: 0.8094 (pm20) cc_final: 0.7839 (pm20) REVERT: I 68 ILE cc_start: 0.8458 (mm) cc_final: 0.8068 (mt) REVERT: K 93 ASP cc_start: 0.8970 (m-30) cc_final: 0.8687 (t0) REVERT: K 102 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8310 (tm-30) REVERT: L 27 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8140 (mm-30) REVERT: L 44 MET cc_start: 0.8840 (mmt) cc_final: 0.8313 (mmt) REVERT: U 40 ASN cc_start: 0.8176 (t0) cc_final: 0.7947 (t0) REVERT: U 71 MET cc_start: 0.7384 (pmm) cc_final: 0.7005 (pmm) REVERT: U 100 PHE cc_start: 0.7920 (t80) cc_final: 0.7648 (t80) REVERT: W 245 MET cc_start: 0.8982 (mmm) cc_final: 0.8678 (mtt) REVERT: W 316 MET cc_start: 0.6869 (ttp) cc_final: 0.6657 (ppp) REVERT: Z 481 ILE cc_start: 0.5173 (OUTLIER) cc_final: 0.4951 (mp) REVERT: D 76 ASN cc_start: 0.5982 (t0) cc_final: 0.5620 (t0) REVERT: G 1 MET cc_start: 0.7195 (tpp) cc_final: 0.6882 (tpp) REVERT: G 63 ARG cc_start: 0.8097 (mmm160) cc_final: 0.7193 (mmm-85) outliers start: 92 outliers final: 46 residues processed: 453 average time/residue: 0.2404 time to fit residues: 187.6483 Evaluate side-chains 402 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 351 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1192 TRP Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain U residue 119 ASP Chi-restraints excluded: chain U residue 173 THR Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 470 LEU Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 559 ASN Chi-restraints excluded: chain W residue 566 ILE Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain G residue 6 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 70 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 281 optimal weight: 0.0670 chunk 59 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 509 optimal weight: 20.0000 chunk 520 optimal weight: 50.0000 chunk 51 optimal weight: 6.9990 chunk 437 optimal weight: 50.0000 chunk 146 optimal weight: 6.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 HIS ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN B 913 GLN ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 GLN B1094 GLN C 66 HIS ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN I 100 HIS U 40 ASN U 142 GLN U 147 ASN U 162 HIS U 188 GLN W 270 GLN W 354 HIS Z 220 HIS ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.119457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.075063 restraints weight = 116421.652| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.91 r_work: 0.2991 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 45835 Z= 0.261 Angle : 0.685 20.088 62177 Z= 0.352 Chirality : 0.046 0.259 6784 Planarity : 0.004 0.070 7864 Dihedral : 14.571 168.275 7243 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.34 % Favored : 94.64 % Rotamer: Outliers : 2.98 % Allowed : 11.76 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.11), residues: 5485 helix: 0.77 (0.11), residues: 2215 sheet: -1.45 (0.18), residues: 726 loop : -1.36 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG I 103 TYR 0.033 0.002 TYR B1048 PHE 0.020 0.002 PHE A 592 TRP 0.018 0.002 TRP B 548 HIS 0.048 0.002 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.26 (45806) covalent geometry : angle 0.67220 / 0.35 (62156) hydrogen bonds : bond 0.03815 / 2.56 ( 2067) hydrogen bonds : angle 4.83641 / 3.37 ( 5851) metal coordination : bond 0.00856 / 0.58 ( 29) metal coordination : angle 7.31625 / 4.67 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 350 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.7790 (ptt) cc_final: 0.7566 (ptp) REVERT: A 118 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8485 (mt) REVERT: A 248 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8136 (mmm) REVERT: A 329 MET cc_start: 0.7875 (ptp) cc_final: 0.7413 (ttp) REVERT: A 469 MET cc_start: 0.9468 (ttt) cc_final: 0.9048 (ttm) REVERT: A 501 MET cc_start: 0.9464 (mtp) cc_final: 0.9144 (mtp) REVERT: A 715 GLU cc_start: 0.8806 (pp20) cc_final: 0.8412 (pp20) REVERT: A 1119 LEU cc_start: 0.8815 (mt) cc_final: 0.8557 (mm) REVERT: A 1230 GLN cc_start: 0.9412 (mt0) cc_final: 0.9149 (mt0) REVERT: A 1361 ASP cc_start: 0.8665 (t0) cc_final: 0.8143 (t0) REVERT: A 1447 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7742 (tt0) REVERT: C 15 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8451 (p) REVERT: C 215 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8621 (mm-30) REVERT: E 52 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8371 (ptp90) REVERT: H 20 LYS cc_start: 0.9088 (tttm) cc_final: 0.8549 (tptp) REVERT: H 42 ASP cc_start: 0.8929 (m-30) cc_final: 0.8356 (m-30) REVERT: I 68 ILE cc_start: 0.8636 (mm) cc_final: 0.8281 (mt) REVERT: I 103 ARG cc_start: 0.7675 (ttt180) cc_final: 0.7008 (ttt90) REVERT: K 1 MET cc_start: 0.8095 (tpt) cc_final: 0.7806 (tpp) REVERT: K 102 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8230 (tm-30) REVERT: K 114 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8254 (pp20) REVERT: L 27 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8166 (mm-30) REVERT: L 44 MET cc_start: 0.8978 (mmt) cc_final: 0.8586 (mmt) REVERT: U 71 MET cc_start: 0.7631 (pmm) cc_final: 0.7327 (pmm) REVERT: U 76 MET cc_start: 0.8679 (mmp) cc_final: 0.8462 (mmp) REVERT: U 100 PHE cc_start: 0.8094 (t80) cc_final: 0.7806 (t80) REVERT: U 125 ARG cc_start: 0.7667 (ttm110) cc_final: 0.6566 (mmm160) REVERT: W 316 MET cc_start: 0.7020 (ttp) cc_final: 0.6772 (ppp) REVERT: W 457 GLU cc_start: 0.9008 (tp30) cc_final: 0.8596 (tp30) REVERT: Y 42 MET cc_start: 0.0386 (mpp) cc_final: -0.0176 (tmm) REVERT: Z 481 ILE cc_start: 0.4819 (OUTLIER) cc_final: 0.4566 (mp) REVERT: D 76 ASN cc_start: 0.6164 (t0) cc_final: 0.5835 (t0) REVERT: D 90 LYS cc_start: 0.5960 (mttm) cc_final: 0.5726 (ptpp) REVERT: G 8 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7104 (mm-30) REVERT: G 63 ARG cc_start: 0.8400 (mmm160) cc_final: 0.7534 (mmm-85) REVERT: G 117 MET cc_start: 0.2476 (mmm) cc_final: 0.1939 (tpp) outliers start: 132 outliers final: 75 residues processed: 459 average time/residue: 0.2477 time to fit residues: 195.5550 Evaluate side-chains 408 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 326 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1192 TRP Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 125 TYR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain U residue 173 THR Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain W residue 189 THR Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 235 GLU Chi-restraints excluded: chain W residue 253 GLN Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 413 THR Chi-restraints excluded: chain W residue 469 VAL Chi-restraints excluded: chain W residue 470 LEU Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 559 ASN Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 596 VAL Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 492 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 305 optimal weight: 0.7980 chunk 470 optimal weight: 9.9990 chunk 528 optimal weight: 40.0000 chunk 542 optimal weight: 30.0000 chunk 513 optimal weight: 0.3980 chunk 506 optimal weight: 6.9990 chunk 514 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 551 optimal weight: 8.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN B 265 GLN ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN B 968 ASN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 HIS ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 80 GLN W 444 GLN Z 220 HIS ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.119641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.075205 restraints weight = 115415.262| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.91 r_work: 0.2999 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 45835 Z= 0.190 Angle : 0.618 18.769 62177 Z= 0.315 Chirality : 0.044 0.259 6784 Planarity : 0.004 0.063 7864 Dihedral : 14.502 169.611 7243 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.87 % Allowed : 12.35 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.11), residues: 5485 helix: 1.04 (0.11), residues: 2211 sheet: -1.35 (0.18), residues: 713 loop : -1.21 (0.12), residues: 2561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 324 TYR 0.021 0.002 TYR B 388 PHE 0.026 0.002 PHE A 312 TRP 0.015 0.001 TRP B 27 HIS 0.019 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (45806) covalent geometry : angle 0.60613 / 0.31 (62156) hydrogen bonds : bond 0.03511 / 2.36 ( 2067) hydrogen bonds : angle 4.68999 / 3.26 ( 5851) metal coordination : bond 0.00605 / 0.40 ( 29) metal coordination : angle 6.46868 / 4.07 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 346 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.7769 (ptt) cc_final: 0.7522 (ptp) REVERT: A 118 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8396 (mt) REVERT: A 248 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8135 (mmm) REVERT: A 329 MET cc_start: 0.7835 (ptp) cc_final: 0.7407 (ttp) REVERT: A 501 MET cc_start: 0.9459 (mtp) cc_final: 0.9077 (mtp) REVERT: A 715 GLU cc_start: 0.8783 (pp20) cc_final: 0.8380 (pp20) REVERT: A 1119 LEU cc_start: 0.8843 (mt) cc_final: 0.8602 (mm) REVERT: A 1230 GLN cc_start: 0.9459 (mt0) cc_final: 0.9243 (mt0) REVERT: A 1288 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8954 (tp) REVERT: A 1361 ASP cc_start: 0.8668 (t0) cc_final: 0.8148 (t70) REVERT: C 15 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8500 (p) REVERT: C 215 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8619 (mm-30) REVERT: E 52 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8381 (ptp90) REVERT: E 65 ASN cc_start: 0.8867 (p0) cc_final: 0.8425 (m-40) REVERT: F 75 MET cc_start: 0.9277 (mtt) cc_final: 0.8695 (mtt) REVERT: H 20 LYS cc_start: 0.9137 (tttm) cc_final: 0.8503 (tptp) REVERT: H 42 ASP cc_start: 0.8941 (m-30) cc_final: 0.8471 (m-30) REVERT: I 68 ILE cc_start: 0.8748 (mm) cc_final: 0.8408 (mt) REVERT: I 103 ARG cc_start: 0.7697 (ttt180) cc_final: 0.7162 (ttt-90) REVERT: K 1 MET cc_start: 0.8072 (tpt) cc_final: 0.7813 (tpp) REVERT: K 93 ASP cc_start: 0.8969 (m-30) cc_final: 0.8717 (t0) REVERT: K 102 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8169 (tm-30) REVERT: K 114 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8248 (pp20) REVERT: L 27 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8120 (mm-30) REVERT: L 44 MET cc_start: 0.8988 (mmt) cc_final: 0.8499 (mmt) REVERT: U 71 MET cc_start: 0.7666 (pmm) cc_final: 0.7378 (pmm) REVERT: U 100 PHE cc_start: 0.8231 (t80) cc_final: 0.8013 (t80) REVERT: W 457 GLU cc_start: 0.8981 (tp30) cc_final: 0.8533 (tp30) REVERT: W 566 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7388 (tp) REVERT: Y 42 MET cc_start: 0.0508 (mpp) cc_final: -0.0144 (tmm) REVERT: Z 481 ILE cc_start: 0.5025 (OUTLIER) cc_final: 0.4817 (mp) REVERT: D 76 ASN cc_start: 0.6128 (t0) cc_final: 0.5778 (t0) REVERT: G 8 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7059 (mm-30) REVERT: G 63 ARG cc_start: 0.8299 (mmm160) cc_final: 0.7749 (mtt180) REVERT: G 78 ARG cc_start: 0.6917 (tpp80) cc_final: 0.6685 (ttm170) outliers start: 127 outliers final: 73 residues processed: 451 average time/residue: 0.2512 time to fit residues: 195.2869 Evaluate side-chains 403 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 322 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1192 TRP Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain U residue 119 ASP Chi-restraints excluded: chain U residue 173 THR Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 413 THR Chi-restraints excluded: chain W residue 469 VAL Chi-restraints excluded: chain W residue 470 LEU Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 559 ASN Chi-restraints excluded: chain W residue 566 ILE Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 359 LEU Chi-restraints excluded: chain Z residue 360 ILE Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 596 VAL Chi-restraints excluded: chain Z residue 743 ILE Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 372 optimal weight: 20.0000 chunk 406 optimal weight: 50.0000 chunk 155 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 290 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 505 optimal weight: 9.9990 chunk 497 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 HIS ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN B 344 GLN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 HIS U 40 ASN Z 220 HIS Z 232 GLN Z 616 HIS Z 632 ASN ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.118674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.074089 restraints weight = 115941.132| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.89 r_work: 0.2968 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 45835 Z= 0.219 Angle : 0.638 18.644 62177 Z= 0.324 Chirality : 0.045 0.252 6784 Planarity : 0.004 0.067 7864 Dihedral : 14.445 168.925 7243 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.93 % Allowed : 12.87 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.12), residues: 5485 helix: 1.19 (0.11), residues: 2213 sheet: -1.26 (0.18), residues: 703 loop : -1.14 (0.12), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 125 TYR 0.022 0.002 TYR B 388 PHE 0.021 0.002 PHE W 317 TRP 0.016 0.001 TRP B 27 HIS 0.012 0.001 HIS G 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 (45806) covalent geometry : angle 0.62647 / 0.32 (62156) hydrogen bonds : bond 0.03505 / 2.37 ( 2067) hydrogen bonds : angle 4.62981 / 3.22 ( 5851) metal coordination : bond 0.00760 / 0.49 ( 29) metal coordination : angle 6.51103 / 4.12 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 328 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.9283 (t0) cc_final: 0.9027 (p0) REVERT: A 118 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8402 (mt) REVERT: A 248 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8241 (mmm) REVERT: A 329 MET cc_start: 0.7903 (ptp) cc_final: 0.7603 (ttp) REVERT: A 469 MET cc_start: 0.9533 (ttp) cc_final: 0.9322 (ttm) REVERT: A 501 MET cc_start: 0.9445 (mtp) cc_final: 0.9078 (mtp) REVERT: A 715 GLU cc_start: 0.8831 (pp20) cc_final: 0.8467 (pp20) REVERT: A 1119 LEU cc_start: 0.8886 (mt) cc_final: 0.8620 (mm) REVERT: A 1230 GLN cc_start: 0.9461 (mt0) cc_final: 0.9137 (mt0) REVERT: A 1288 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8981 (tp) REVERT: A 1361 ASP cc_start: 0.8704 (t0) cc_final: 0.8264 (t70) REVERT: B 163 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9255 (pp) REVERT: B 265 GLN cc_start: 0.6806 (pt0) cc_final: 0.6590 (pt0) REVERT: B 1151 MET cc_start: 0.9495 (ptt) cc_final: 0.8688 (ptt) REVERT: C 15 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8560 (p) REVERT: C 215 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8640 (mm-30) REVERT: E 52 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8401 (ptp90) REVERT: E 65 ASN cc_start: 0.8875 (p0) cc_final: 0.8552 (m-40) REVERT: E 90 TYR cc_start: 0.8628 (m-80) cc_final: 0.8168 (m-80) REVERT: H 20 LYS cc_start: 0.9134 (tttm) cc_final: 0.8637 (tptp) REVERT: H 42 ASP cc_start: 0.8955 (m-30) cc_final: 0.8505 (m-30) REVERT: I 68 ILE cc_start: 0.8785 (mm) cc_final: 0.8478 (mt) REVERT: I 103 ARG cc_start: 0.7678 (ttt180) cc_final: 0.7146 (ttt-90) REVERT: K 93 ASP cc_start: 0.8959 (m-30) cc_final: 0.8691 (t0) REVERT: K 102 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8185 (tm-30) REVERT: K 114 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8259 (pp20) REVERT: U 71 MET cc_start: 0.7758 (pmm) cc_final: 0.7529 (pmm) REVERT: U 100 PHE cc_start: 0.8281 (t80) cc_final: 0.7939 (t80) REVERT: U 125 ARG cc_start: 0.7767 (ttm110) cc_final: 0.7013 (mmm160) REVERT: W 230 MET cc_start: 0.8085 (mtm) cc_final: 0.7816 (ptp) REVERT: W 316 MET cc_start: 0.7186 (ppp) cc_final: 0.6767 (ppp) REVERT: Z 357 ASP cc_start: 0.0987 (m-30) cc_final: 0.0784 (p0) REVERT: Z 481 ILE cc_start: 0.5015 (OUTLIER) cc_final: 0.4799 (mp) REVERT: D 76 ASN cc_start: 0.6193 (t0) cc_final: 0.5859 (t0) REVERT: G 63 ARG cc_start: 0.8306 (mmm160) cc_final: 0.7916 (mtm-85) REVERT: G 104 MET cc_start: 0.4874 (tpt) cc_final: 0.4129 (mmm) REVERT: G 117 MET cc_start: 0.2654 (mmm) cc_final: 0.2050 (tpp) outliers start: 130 outliers final: 81 residues processed: 437 average time/residue: 0.2354 time to fit residues: 177.3931 Evaluate side-chains 406 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 317 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 119 ASP Chi-restraints excluded: chain U residue 173 THR Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain W residue 189 THR Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 413 THR Chi-restraints excluded: chain W residue 470 LEU Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 559 ASN Chi-restraints excluded: chain W residue 575 VAL Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 360 ILE Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 730 SER Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 145 optimal weight: 8.9990 chunk 256 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 464 optimal weight: 3.9990 chunk 333 optimal weight: 1.9990 chunk 230 optimal weight: 0.0470 chunk 501 optimal weight: 30.0000 chunk 341 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 GLN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 80 GLN Z 220 HIS Z 232 GLN ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.120094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.075777 restraints weight = 114924.094| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.88 r_work: 0.3009 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 45835 Z= 0.128 Angle : 0.590 16.242 62177 Z= 0.300 Chirality : 0.043 0.253 6784 Planarity : 0.004 0.055 7864 Dihedral : 14.344 170.155 7242 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.30 % Allowed : 13.63 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.12 (0.12), residues: 5485 helix: 1.37 (0.12), residues: 2226 sheet: -1.14 (0.18), residues: 721 loop : -1.05 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 125 TYR 0.020 0.001 TYR W 238 PHE 0.017 0.001 PHE I 96 TRP 0.014 0.001 TRP C 203 HIS 0.011 0.001 HIS I 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (45806) covalent geometry : angle 0.58142 / 0.30 (62156) hydrogen bonds : bond 0.03217 / 2.18 ( 2067) hydrogen bonds : angle 4.46294 / 3.10 ( 5851) metal coordination : bond 0.00401 / 0.28 ( 29) metal coordination : angle 5.44278 / 3.38 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 330 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8394 (mt) REVERT: A 248 MET cc_start: 0.8809 (mmm) cc_final: 0.8461 (mmm) REVERT: A 329 MET cc_start: 0.7869 (ptp) cc_final: 0.7567 (ttp) REVERT: A 469 MET cc_start: 0.9468 (ttp) cc_final: 0.9077 (ttm) REVERT: A 501 MET cc_start: 0.9420 (mtp) cc_final: 0.9026 (mtp) REVERT: A 565 MET cc_start: 0.9513 (mmm) cc_final: 0.9054 (mmm) REVERT: A 579 ILE cc_start: 0.9471 (OUTLIER) cc_final: 0.9213 (mm) REVERT: A 715 GLU cc_start: 0.8779 (pp20) cc_final: 0.8371 (pp20) REVERT: A 1230 GLN cc_start: 0.9486 (mt0) cc_final: 0.9211 (mt0) REVERT: A 1288 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8974 (tp) REVERT: A 1361 ASP cc_start: 0.8689 (t0) cc_final: 0.8273 (t70) REVERT: B 163 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9091 (pp) REVERT: B 315 ASN cc_start: 0.9024 (m-40) cc_final: 0.8757 (p0) REVERT: B 1151 MET cc_start: 0.9502 (ptt) cc_final: 0.8777 (ptt) REVERT: C 15 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8612 (p) REVERT: C 59 LEU cc_start: 0.9301 (mt) cc_final: 0.9075 (mt) REVERT: C 215 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8619 (mm-30) REVERT: E 27 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8752 (mm) REVERT: E 65 ASN cc_start: 0.8937 (p0) cc_final: 0.8668 (m-40) REVERT: E 90 TYR cc_start: 0.8697 (m-80) cc_final: 0.8250 (m-80) REVERT: H 20 LYS cc_start: 0.9112 (tttm) cc_final: 0.8656 (tptp) REVERT: H 42 ASP cc_start: 0.8883 (m-30) cc_final: 0.8454 (m-30) REVERT: H 124 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8159 (ttp80) REVERT: I 68 ILE cc_start: 0.8707 (mm) cc_final: 0.8405 (mt) REVERT: I 100 HIS cc_start: 0.7861 (OUTLIER) cc_final: 0.7392 (t-170) REVERT: I 103 ARG cc_start: 0.7623 (ttt180) cc_final: 0.7187 (ttt-90) REVERT: K 93 ASP cc_start: 0.8887 (m-30) cc_final: 0.8634 (t0) REVERT: K 102 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8154 (tm-30) REVERT: K 114 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8255 (pp20) REVERT: U 125 ARG cc_start: 0.7700 (ttm110) cc_final: 0.7124 (mtm-85) REVERT: W 264 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: W 338 MET cc_start: 0.8553 (tpp) cc_final: 0.8317 (tpp) REVERT: Y 42 MET cc_start: 0.0668 (mpp) cc_final: -0.0521 (tmm) REVERT: Z 481 ILE cc_start: 0.4991 (OUTLIER) cc_final: 0.4786 (mp) REVERT: D 76 ASN cc_start: 0.6059 (t0) cc_final: 0.5699 (t0) REVERT: D 90 LYS cc_start: 0.6732 (ptpp) cc_final: 0.6349 (pttm) REVERT: G 63 ARG cc_start: 0.8199 (mmm160) cc_final: 0.7820 (mmm-85) REVERT: G 104 MET cc_start: 0.4635 (tpt) cc_final: 0.4062 (mmm) outliers start: 102 outliers final: 68 residues processed: 420 average time/residue: 0.2437 time to fit residues: 175.2570 Evaluate side-chains 386 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 307 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain U residue 119 ASP Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 264 GLU Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 470 LEU Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 559 ASN Chi-restraints excluded: chain W residue 589 VAL Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 360 ILE Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 743 ILE Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 509 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 214 optimal weight: 6.9990 chunk 229 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 196 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 533 optimal weight: 9.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 HIS Z 220 HIS Z 232 GLN ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.119610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.075193 restraints weight = 115745.380| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.89 r_work: 0.2998 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 45835 Z= 0.152 Angle : 0.595 14.750 62177 Z= 0.302 Chirality : 0.043 0.250 6784 Planarity : 0.004 0.060 7864 Dihedral : 14.266 169.113 7242 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.33 % Allowed : 13.57 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.01 (0.12), residues: 5485 helix: 1.45 (0.12), residues: 2227 sheet: -1.00 (0.19), residues: 673 loop : -0.98 (0.12), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 583 TYR 0.017 0.001 TYR B 84 PHE 0.024 0.001 PHE W 240 TRP 0.014 0.001 TRP B 27 HIS 0.005 0.001 HIS Z 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (45806) covalent geometry : angle 0.58724 / 0.30 (62156) hydrogen bonds : bond 0.03211 / 2.17 ( 2067) hydrogen bonds : angle 4.41175 / 3.06 ( 5851) metal coordination : bond 0.00527 / 0.33 ( 29) metal coordination : angle 5.22305 / 3.29 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 324 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8383 (mt) REVERT: A 248 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8237 (mmm) REVERT: A 329 MET cc_start: 0.7934 (ptp) cc_final: 0.7648 (ttp) REVERT: A 469 MET cc_start: 0.9480 (ttp) cc_final: 0.9240 (ttm) REVERT: A 501 MET cc_start: 0.9400 (mtp) cc_final: 0.9047 (mtp) REVERT: A 579 ILE cc_start: 0.9477 (OUTLIER) cc_final: 0.9207 (mm) REVERT: A 715 GLU cc_start: 0.8819 (pp20) cc_final: 0.8449 (pp20) REVERT: A 1230 GLN cc_start: 0.9518 (mt0) cc_final: 0.9252 (mt0) REVERT: A 1361 ASP cc_start: 0.8662 (t0) cc_final: 0.8276 (t70) REVERT: B 163 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9060 (pp) REVERT: B 265 GLN cc_start: 0.6569 (pt0) cc_final: 0.4995 (pt0) REVERT: B 315 ASN cc_start: 0.9064 (m-40) cc_final: 0.8791 (p0) REVERT: B 1145 GLN cc_start: 0.8548 (mp-120) cc_final: 0.8288 (mp10) REVERT: B 1151 MET cc_start: 0.9519 (ptt) cc_final: 0.8798 (ptt) REVERT: C 15 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8605 (p) REVERT: C 215 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8637 (mm-30) REVERT: E 27 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8889 (mm) REVERT: E 90 TYR cc_start: 0.8754 (m-80) cc_final: 0.8280 (m-80) REVERT: F 82 GLU cc_start: 0.7792 (pp20) cc_final: 0.7560 (pp20) REVERT: H 20 LYS cc_start: 0.9116 (tttm) cc_final: 0.8538 (tptp) REVERT: H 42 ASP cc_start: 0.8870 (m-30) cc_final: 0.8414 (m-30) REVERT: H 124 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8248 (ttp80) REVERT: I 68 ILE cc_start: 0.8739 (mm) cc_final: 0.8450 (mt) REVERT: K 93 ASP cc_start: 0.8919 (m-30) cc_final: 0.8660 (t0) REVERT: K 102 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8141 (tm-30) REVERT: K 114 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8247 (pp20) REVERT: U 71 MET cc_start: 0.8026 (pmm) cc_final: 0.7746 (pmm) REVERT: U 125 ARG cc_start: 0.7738 (ttm110) cc_final: 0.7089 (mtm-85) REVERT: W 245 MET cc_start: 0.9112 (mtp) cc_final: 0.8896 (mtp) REVERT: W 264 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: Y 42 MET cc_start: 0.0565 (mpp) cc_final: -0.0508 (tmm) REVERT: Z 481 ILE cc_start: 0.4991 (OUTLIER) cc_final: 0.4775 (mp) REVERT: D 76 ASN cc_start: 0.6067 (t0) cc_final: 0.5648 (t0) REVERT: D 90 LYS cc_start: 0.6384 (ptpp) cc_final: 0.6036 (pttm) REVERT: G 63 ARG cc_start: 0.8267 (mmm160) cc_final: 0.7913 (mmm-85) REVERT: G 104 MET cc_start: 0.4942 (tpt) cc_final: 0.4369 (mmm) outliers start: 103 outliers final: 70 residues processed: 413 average time/residue: 0.2334 time to fit residues: 166.5818 Evaluate side-chains 389 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 309 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 792 ASP Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain U residue 119 ASP Chi-restraints excluded: chain U residue 173 THR Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain W residue 264 GLU Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 470 LEU Chi-restraints excluded: chain W residue 512 VAL Chi-restraints excluded: chain W residue 559 ASN Chi-restraints excluded: chain W residue 589 VAL Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 360 ILE Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 743 ILE Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 482 optimal weight: 0.0670 chunk 507 optimal weight: 40.0000 chunk 306 optimal weight: 0.9990 chunk 257 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 354 optimal weight: 50.0000 chunk 240 optimal weight: 0.9980 chunk 471 optimal weight: 0.8980 chunk 472 optimal weight: 5.9990 chunk 267 optimal weight: 3.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 HIS K 69 HIS ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 80 GLN Z 178 ASN Z 220 HIS Z 232 GLN ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.120301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.076125 restraints weight = 115146.754| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.88 r_work: 0.3020 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 45835 Z= 0.118 Angle : 0.584 14.015 62177 Z= 0.296 Chirality : 0.043 0.337 6784 Planarity : 0.003 0.050 7864 Dihedral : 14.224 169.728 7242 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.90 % Allowed : 14.33 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.12), residues: 5485 helix: 1.51 (0.12), residues: 2236 sheet: -0.98 (0.19), residues: 684 loop : -0.93 (0.12), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 42 TYR 0.016 0.001 TYR W 415 PHE 0.028 0.001 PHE C 63 TRP 0.012 0.001 TRP C 203 HIS 0.015 0.001 HIS I 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (45806) covalent geometry : angle 0.57691 / 0.30 (62156) hydrogen bonds : bond 0.03082 / 2.09 ( 2067) hydrogen bonds : angle 4.33928 / 3.01 ( 5851) metal coordination : bond 0.00362 / 0.25 ( 29) metal coordination : angle 4.92128 / 3.08 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 322 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8360 (mt) REVERT: A 248 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8148 (mmm) REVERT: A 329 MET cc_start: 0.7951 (ptp) cc_final: 0.7675 (ttp) REVERT: A 469 MET cc_start: 0.9467 (ttp) cc_final: 0.9255 (ttm) REVERT: A 501 MET cc_start: 0.9390 (mtp) cc_final: 0.9009 (mtp) REVERT: A 561 MET cc_start: 0.9085 (mtt) cc_final: 0.8883 (mtt) REVERT: A 565 MET cc_start: 0.9507 (mmm) cc_final: 0.9265 (mmm) REVERT: A 579 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.9204 (mm) REVERT: A 712 ASP cc_start: 0.8881 (t0) cc_final: 0.8519 (t0) REVERT: A 715 GLU cc_start: 0.8778 (pp20) cc_final: 0.8448 (pp20) REVERT: A 1230 GLN cc_start: 0.9526 (mt0) cc_final: 0.9270 (mt0) REVERT: B 163 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.8899 (pp) REVERT: B 315 ASN cc_start: 0.9084 (m-40) cc_final: 0.8808 (p0) REVERT: B 420 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7691 (mm-40) REVERT: B 1145 GLN cc_start: 0.8558 (mp-120) cc_final: 0.8280 (mp10) REVERT: B 1151 MET cc_start: 0.9483 (ptt) cc_final: 0.8740 (ptt) REVERT: C 15 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8572 (p) REVERT: C 215 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8636 (mm-30) REVERT: E 27 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8818 (mm) REVERT: E 90 TYR cc_start: 0.8716 (m-80) cc_final: 0.8324 (m-80) REVERT: E 121 MET cc_start: 0.8265 (pmm) cc_final: 0.8046 (pmm) REVERT: F 94 MET cc_start: 0.9189 (mmm) cc_final: 0.8846 (mmm) REVERT: H 20 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8589 (tptp) REVERT: H 42 ASP cc_start: 0.8860 (m-30) cc_final: 0.8398 (m-30) REVERT: H 124 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8173 (ttp80) REVERT: K 93 ASP cc_start: 0.8885 (m-30) cc_final: 0.8658 (t0) REVERT: K 97 GLU cc_start: 0.8757 (tt0) cc_final: 0.8529 (tt0) REVERT: K 102 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8117 (tm-30) REVERT: K 114 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8271 (pp20) REVERT: U 39 ASP cc_start: 0.9001 (p0) cc_final: 0.8765 (p0) REVERT: U 125 ARG cc_start: 0.7678 (ttm110) cc_final: 0.7116 (mtm-85) REVERT: W 264 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: W 457 GLU cc_start: 0.8998 (tp30) cc_final: 0.8631 (tt0) REVERT: Y 42 MET cc_start: 0.0316 (mpp) cc_final: -0.0779 (tmm) REVERT: Z 481 ILE cc_start: 0.4973 (OUTLIER) cc_final: 0.4770 (mp) REVERT: D 76 ASN cc_start: 0.6099 (t0) cc_final: 0.5791 (t0) REVERT: D 90 LYS cc_start: 0.6324 (ptpp) cc_final: 0.5958 (pttm) REVERT: G 104 MET cc_start: 0.5007 (tpt) cc_final: 0.4408 (mmm) outliers start: 84 outliers final: 61 residues processed: 393 average time/residue: 0.2148 time to fit residues: 145.4199 Evaluate side-chains 381 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 309 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain U residue 119 ASP Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 244 MET Chi-restraints excluded: chain W residue 264 GLU Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 470 LEU Chi-restraints excluded: chain W residue 559 ASN Chi-restraints excluded: chain W residue 589 VAL Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 360 ILE Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 743 ILE Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 219 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 232 optimal weight: 4.9990 chunk 543 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 361 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 140 optimal weight: 0.0980 chunk 560 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 220 HIS Z 232 GLN ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.119599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.075223 restraints weight = 115640.477| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.89 r_work: 0.3000 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 45835 Z= 0.154 Angle : 0.605 14.228 62177 Z= 0.305 Chirality : 0.043 0.250 6784 Planarity : 0.004 0.057 7864 Dihedral : 14.199 168.912 7242 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.78 % Allowed : 14.65 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.12), residues: 5485 helix: 1.52 (0.12), residues: 2237 sheet: -0.93 (0.19), residues: 673 loop : -0.89 (0.12), residues: 2575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG B 324 TYR 0.016 0.001 TYR W 415 PHE 0.016 0.001 PHE A 592 TRP 0.013 0.001 TRP B 27 HIS 0.008 0.001 HIS U 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (45806) covalent geometry : angle 0.59715 / 0.30 (62156) hydrogen bonds : bond 0.03158 / 2.13 ( 2067) hydrogen bonds : angle 4.33132 / 3.01 ( 5851) metal coordination : bond 0.00491 / 0.34 ( 29) metal coordination : angle 5.25178 / 3.32 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10970 Ramachandran restraints generated. 5485 Oldfield, 0 Emsley, 5485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 313 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8394 (mt) REVERT: A 248 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8509 (mmm) REVERT: A 317 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7623 (tpp) REVERT: A 329 MET cc_start: 0.7954 (ptp) cc_final: 0.7693 (ttp) REVERT: A 469 MET cc_start: 0.9494 (ttp) cc_final: 0.9292 (ttm) REVERT: A 501 MET cc_start: 0.9384 (mtp) cc_final: 0.9029 (mtp) REVERT: A 565 MET cc_start: 0.9538 (mmm) cc_final: 0.9294 (mmm) REVERT: A 579 ILE cc_start: 0.9464 (OUTLIER) cc_final: 0.9189 (mm) REVERT: A 712 ASP cc_start: 0.8908 (t0) cc_final: 0.8580 (t0) REVERT: A 715 GLU cc_start: 0.8832 (pp20) cc_final: 0.8508 (pp20) REVERT: A 1230 GLN cc_start: 0.9536 (mt0) cc_final: 0.9251 (mt0) REVERT: B 163 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9026 (pp) REVERT: B 315 ASN cc_start: 0.9126 (m-40) cc_final: 0.8814 (p0) REVERT: B 420 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7712 (mm-40) REVERT: B 1145 GLN cc_start: 0.8558 (mp-120) cc_final: 0.8231 (mp10) REVERT: B 1151 MET cc_start: 0.9545 (ptt) cc_final: 0.8830 (ptt) REVERT: C 15 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8621 (p) REVERT: C 215 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8653 (mm-30) REVERT: E 27 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8850 (mm) REVERT: F 94 MET cc_start: 0.9207 (mmm) cc_final: 0.8845 (mmm) REVERT: H 20 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8601 (tptp) REVERT: H 42 ASP cc_start: 0.8881 (m-30) cc_final: 0.8428 (m-30) REVERT: H 124 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8231 (ttp80) REVERT: K 93 ASP cc_start: 0.8900 (m-30) cc_final: 0.8677 (t0) REVERT: K 97 GLU cc_start: 0.8814 (tt0) cc_final: 0.8592 (tt0) REVERT: K 102 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8133 (tm-30) REVERT: K 114 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8273 (pp20) REVERT: U 118 GLN cc_start: 0.7674 (mm110) cc_final: 0.7328 (mm110) REVERT: U 125 ARG cc_start: 0.7684 (ttm110) cc_final: 0.7130 (mtm-85) REVERT: W 264 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: Y 42 MET cc_start: 0.0284 (mpp) cc_final: -0.0795 (tmm) REVERT: Z 481 ILE cc_start: 0.4984 (OUTLIER) cc_final: 0.4780 (mp) REVERT: D 76 ASN cc_start: 0.6240 (t0) cc_final: 0.5949 (t0) REVERT: D 90 LYS cc_start: 0.6306 (ptpp) cc_final: 0.5962 (pttm) REVERT: G 104 MET cc_start: 0.5013 (tpt) cc_final: 0.4406 (mmm) REVERT: G 117 MET cc_start: 0.2493 (mmm) cc_final: 0.0200 (mtm) outliers start: 79 outliers final: 61 residues processed: 377 average time/residue: 0.1987 time to fit residues: 129.8006 Evaluate side-chains 377 residues out of total 4941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 304 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 694 THR Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 225 LYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain U residue 119 ASP Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain W residue 264 GLU Chi-restraints excluded: chain W residue 330 VAL Chi-restraints excluded: chain W residue 470 LEU Chi-restraints excluded: chain W residue 559 ASN Chi-restraints excluded: chain W residue 589 VAL Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 360 ILE Chi-restraints excluded: chain Z residue 481 ILE Chi-restraints excluded: chain Z residue 743 ILE Chi-restraints excluded: chain G residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 566 random chunks: chunk 411 optimal weight: 50.0000 chunk 539 optimal weight: 9.9990 chunk 527 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 541 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 313 optimal weight: 6.9990 chunk 495 optimal weight: 40.0000 chunk 270 optimal weight: 2.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 GLN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 80 GLN W 352 HIS Z 220 HIS ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.118556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.074780 restraints weight = 116091.505| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.13 r_work: 0.2952 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 45835 Z= 0.188 Angle : 0.619 15.853 62177 Z= 0.312 Chirality : 0.044 0.248 6784 Planarity : 0.004 0.067 7864 Dihedral : 14.199 168.480 7242 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.99 % Allowed : 14.42 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.12), residues: 5485 helix: 1.47 (0.12), residues: 2252 sheet: -0.93 (0.19), residues: 666 loop : -0.87 (0.13), residues: 2567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 349 TYR 0.015 0.001 TYR A 187 PHE 0.018 0.001 PHE W 240 TRP 0.014 0.001 TRP B 27 HIS 0.006 0.001 HIS A 804 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (45806) covalent geometry : angle 0.60954 / 0.31 (62156) hydrogen bonds : bond 0.03296 / 2.22 ( 2067) hydrogen bonds : angle 4.36801 / 3.03 ( 5851) metal coordination : bond 0.00639 / 0.42 ( 29) metal coordination : angle 5.88995 / 3.74 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12459.01 seconds wall clock time: 213 minutes 18.91 seconds (12798.91 seconds total)