Starting phenix.real_space_refine on Sun Aug 9 09:10:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kd9_62266/08_2026/9kd9_62266.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kd9_62266/08_2026/9kd9_62266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kd9_62266/08_2026/9kd9_62266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kd9_62266/08_2026/9kd9_62266.map" model { file = "/net/cci-nas-00/data/ceres_data/9kd9_62266/08_2026/9kd9_62266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kd9_62266/08_2026/9kd9_62266.cif" } resolution = 2.88 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 58 5.49 5 Mg 1 5.21 5 S 180 5.16 5 C 20607 2.51 5 N 5734 2.21 5 O 6368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32956 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 11153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1418, 11153 Classifications: {'peptide': 1418} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1351} Chain breaks: 4 Chain: "B" Number of atoms: 9378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9378 Classifications: {'peptide': 1176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1123} Chain breaks: 5 Chain: "C" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "D" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1332 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'NMCIS': 1, 'NMTRANS': 1, 'PCIS': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'SAR:plan-1': 1, 'MVA:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "M" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 56 Unusual residues: {'PXZ': 1} Classifications: {'peptide': 5, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'NMCIS': 1, 'NMTRANS': 1, 'PCIS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="PXZ M 6 " pdbres="THR M 7 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'PXZ:plan-1': 1, 'PXZ:plan-2': 1, 'SAR:plan-1': 1, 'MVA:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 369 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain breaks: 1 Chain: "P" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 4} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Link IDs: {'rna3p': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 820 SG CYS A 107 93.780 84.432 124.028 1.00134.44 S ATOM 844 SG CYS A 110 96.174 81.552 124.637 1.00145.39 S ATOM 1149 SG CYS A 148 93.363 82.102 127.032 1.00161.54 S ATOM 1287 SG CYS A 167 96.197 84.689 126.846 1.00150.07 S ATOM 515 SG CYS A 67 109.962 78.527 80.168 1.00125.07 S ATOM 537 SG CYS A 70 109.862 74.824 79.543 1.00139.79 S ATOM 590 SG CYS A 77 106.603 76.797 79.948 1.00141.25 S ATOM 20037 SG CYS B1163 106.589 66.596 93.353 1.00127.37 S ATOM 20055 SG CYS B1166 105.049 69.651 94.810 1.00117.61 S ATOM 20180 SG CYS B1182 108.326 69.888 92.614 1.00113.21 S ATOM 20199 SG CYS B1185 108.296 68.567 96.184 1.00136.31 S ATOM 21178 SG CYS C 86 81.549 68.702 18.194 1.00125.09 S ATOM 21195 SG CYS C 88 83.360 71.676 19.792 1.00140.98 S ATOM 21228 SG CYS C 92 81.751 71.875 16.270 1.00127.72 S ATOM 21251 SG CYS C 95 79.631 71.759 19.428 1.00116.50 S ATOM 28918 SG CYS I 7 38.473 123.902 119.908 1.00172.59 S ATOM 28943 SG CYS I 10 42.304 124.324 119.603 1.00166.04 S ATOM 29109 SG CYS I 29 40.948 121.287 121.369 1.00177.28 S ATOM 29133 SG CYS I 32 40.504 124.772 122.867 1.00180.85 S ATOM 29460 SG CYS I 75 13.007 105.860 88.574 1.00 98.51 S ATOM 29482 SG CYS I 78 11.547 109.465 87.833 1.00116.16 S ATOM 29698 SG CYS I 103 14.838 108.146 86.170 1.00 96.82 S ATOM 29718 SG CYS I 106 14.471 109.027 89.864 1.00 87.16 S ATOM 29863 SG CYS J 7 53.056 79.927 34.236 1.00 81.55 S ATOM 29886 SG CYS J 10 52.483 77.331 31.476 1.00 78.31 S ATOM 30166 SG CYS J 45 49.834 78.037 34.138 1.00 78.01 S ATOM 30172 SG CYS J 46 50.715 80.396 31.148 1.00 65.23 S ATOM 31352 SG CYS L 31 82.093 112.200 39.083 1.00 86.08 S ATOM 31372 SG CYS L 34 81.290 115.253 36.594 1.00 80.91 S ATOM 31476 SG CYS L 48 84.837 114.300 37.683 1.00 85.77 S ATOM 31499 SG CYS L 51 82.288 115.955 39.933 1.00102.59 S Time building chain proxies: 6.11, per 1000 atoms: 0.19 Number of scatterers: 32956 At special positions: 0 Unit cell: (164.61, 159.96, 151.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 180 16.00 P 58 15.00 Mg 1 11.99 O 6368 8.00 N 5734 7.00 C 20607 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=4, symmetry=0 Links applied TRANS " DVA M 2 " - " THR M 1 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " Number of angles added : 45 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DVA M 2 " pdb=" CB DVA M 8 " Number of C-beta restraints generated: 7498 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 49 sheets defined 38.3% alpha, 19.5% beta 24 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 121 through 128 removed outlier: 3.592A pdb=" N ILE A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 283 Processing helix chain 'A' and resid 285 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.736A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 535 Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.844A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 659 Processing helix chain 'A' and resid 666 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.516A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 846 Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.809A pdb=" N LEU A 913 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.581A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 Processing helix chain 'A' and resid 1004 through 1026 removed outlier: 5.107A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1078 Proline residue: A1075 - end of helix removed outlier: 3.536A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1106 removed outlier: 3.806A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1125 removed outlier: 3.549A pdb=" N ALA A1125 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1177 removed outlier: 3.754A pdb=" N ILE A1170 " --> pdb=" O ASP A1166 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1186 No H-bonds generated for 'chain 'A' and resid 1184 through 1186' Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1251 through 1270 removed outlier: 3.802A pdb=" N GLU A1255 " --> pdb=" O GLU A1251 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASP A1257 " --> pdb=" O GLU A1253 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N HIS A1258 " --> pdb=" O ALA A1254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A1269 " --> pdb=" O ASN A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1318 removed outlier: 3.676A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1339 Processing helix chain 'A' and resid 1340 through 1359 removed outlier: 4.499A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.958A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 Processing helix chain 'A' and resid 1395 through 1400 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1430 removed outlier: 3.654A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1454 removed outlier: 3.784A pdb=" N MET A1454 " --> pdb=" O LEU A1450 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 41 removed outlier: 4.309A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 79 through 82 removed outlier: 3.581A pdb=" N ASP B 82 " --> pdb=" O THR B 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 82' Processing helix chain 'B' and resid 113 through 121 removed outlier: 5.474A pdb=" N LEU B 119 " --> pdb=" O GLN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 307 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 removed outlier: 4.523A pdb=" N ILE B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 Processing helix chain 'B' and resid 449 through 463 removed outlier: 4.214A pdb=" N ILE B 453 " --> pdb=" O ASN B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 592 through 606 Processing helix chain 'B' and resid 654 through 669 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.589A pdb=" N GLU B 699 " --> pdb=" O GLU B 696 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.652A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.091A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.513A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 810 removed outlier: 3.979A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.140A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.760A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1141 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1197 through 1209 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.675A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 267 Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 170 removed outlier: 3.532A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 217 Processing helix chain 'E' and resid 3 through 27 removed outlier: 3.620A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.679A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 117 through 122 removed outlier: 3.683A pdb=" N LYS E 122 " --> pdb=" O PRO E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 removed outlier: 3.514A pdb=" N HIS E 146 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.689A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.709A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.538A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 56 through 63 removed outlier: 3.983A pdb=" N TYR J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.855A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.734A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.476A pdb=" N LYS A 88 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N ILE A 235 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 removed outlier: 3.609A pdb=" N LYS A 180 " --> pdb=" O ASP A 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.536A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.535A pdb=" N LYS A 431 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL A 405 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU A 433 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.551A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 567 removed outlier: 6.112A pdb=" N VAL H 96 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.470A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB4, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AB5, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AB6, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB7, first strand: chain 'A' and resid 1281 through 1292 removed outlier: 3.738A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 6.159A pdb=" N ILE A1238 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU A1193 " --> pdb=" O ILE A1238 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N CYS A1240 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TRP A1191 " --> pdb=" O CYS A1240 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL A1242 " --> pdb=" O SER A1189 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AC1, first strand: chain 'B' and resid 68 through 73 removed outlier: 5.321A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 68 through 73 removed outlier: 5.321A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 101 through 102 removed outlier: 3.559A pdb=" N HIS B 110 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC5, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AC6, first strand: chain 'B' and resid 223 through 227 removed outlier: 3.961A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC8, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC9, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.293A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.715A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.715A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD4, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.652A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD6, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.541A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD8, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD9, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.507A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 119 through 120 removed outlier: 3.535A pdb=" N VAL C 119 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.774A pdb=" N HIS C 131 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE4, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 Processing sheet with id=AE6, first strand: chain 'E' and resid 87 through 88 removed outlier: 3.732A pdb=" N VAL E 88 " --> pdb=" O ASN E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE8, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.628A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 85 through 94 removed outlier: 6.870A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE G 109 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY G 161 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS G 158 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AF2, first strand: chain 'I' and resid 14 through 18 Processing sheet with id=AF3, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AF4, first strand: chain 'K' and resid 19 through 23 1412 hydrogen bonds defined for protein. 3894 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 7.71 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5516 1.31 - 1.44: 8639 1.44 - 1.57: 19103 1.57 - 1.69: 115 1.69 - 1.82: 288 Bond restraints: 33661 Sorted by residual: bond pdb=" C12 PXZ M 6 " pdb=" C4 PXZ M 6 " ideal model delta sigma weight residual 1.354 1.542 -0.188 2.00e-02 2.50e+03 8.84e+01 bond pdb=" C1 PXZ M 6 " pdb=" C2 PXZ M 6 " ideal model delta sigma weight residual 1.372 1.520 -0.148 2.00e-02 2.50e+03 5.47e+01 bond pdb=" C2 PXZ M 6 " pdb=" N2 PXZ M 6 " ideal model delta sigma weight residual 1.344 1.467 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C11 PXZ M 6 " pdb=" N10 PXZ M 6 " ideal model delta sigma weight residual 1.297 1.418 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" C13 PXZ M 6 " pdb=" O5 PXZ M 6 " ideal model delta sigma weight residual 1.353 1.471 -0.118 2.00e-02 2.50e+03 3.49e+01 ... (remaining 33656 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 44705 1.69 - 3.38: 883 3.38 - 5.07: 98 5.07 - 6.76: 12 6.76 - 8.45: 5 Bond angle restraints: 45703 Sorted by residual: angle pdb=" O4' DG N 32 " pdb=" C1' DG N 32 " pdb=" N9 DG N 32 " ideal model delta sigma weight residual 108.00 112.72 -4.72 7.00e-01 2.04e+00 4.54e+01 angle pdb=" O4' DT T 22 " pdb=" C4' DT T 22 " pdb=" C3' DT T 22 " ideal model delta sigma weight residual 106.00 102.83 3.17 6.00e-01 2.78e+00 2.79e+01 angle pdb=" CA MVA M 11 " pdb=" C MVA M 11 " pdb=" O MVA M 11 " ideal model delta sigma weight residual 120.80 113.01 7.79 1.70e+00 3.46e-01 2.10e+01 angle pdb=" N3 DT T 16 " pdb=" C4 DT T 16 " pdb=" O4 DT T 16 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT T 21 " pdb=" C4 DT T 21 " pdb=" O4 DT T 21 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 ... (remaining 45698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.58: 19849 31.58 - 63.16: 597 63.16 - 94.74: 46 94.74 - 126.32: 0 126.32 - 157.90: 5 Dihedral angle restraints: 20497 sinusoidal: 8917 harmonic: 11580 Sorted by residual: dihedral pdb=" C SAR M 4 " pdb=" N SAR M 4 " pdb=" CA SAR M 4 " pdb=" CN SAR M 4 " ideal model delta sinusoidal sigma weight residual 71.89 -86.01 157.90 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C SAR M 10 " pdb=" N SAR M 10 " pdb=" CA SAR M 10 " pdb=" CN SAR M 10 " ideal model delta sinusoidal sigma weight residual 71.89 -81.62 153.51 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" CA PRO I 76 " pdb=" C PRO I 76 " pdb=" N LYS I 77 " pdb=" CA LYS I 77 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 20494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4017 0.051 - 0.101: 921 0.101 - 0.152: 196 0.152 - 0.203: 3 0.203 - 0.253: 3 Chirality restraints: 5140 Sorted by residual: chirality pdb=" CA DVA M 8 " pdb=" N DVA M 8 " pdb=" C DVA M 8 " pdb=" CB DVA M 8 " both_signs ideal model delta sigma weight residual False -2.44 -2.19 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA MVA M 11 " pdb=" N MVA M 11 " pdb=" C MVA M 11 " pdb=" CB MVA M 11 " both_signs ideal model delta sigma weight residual False 2.44 2.20 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA DVA M 2 " pdb=" N DVA M 2 " pdb=" C DVA M 2 " pdb=" CB DVA M 2 " both_signs ideal model delta sigma weight residual False -2.44 -2.23 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 5137 not shown) Planarity restraints: 5724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C0 PXZ M 6 " 0.021 2.00e-02 2.50e+03 2.75e-02 3.78e+01 pdb=" C0' PXZ M 6 " -0.008 2.00e-02 2.50e+03 pdb=" C1 PXZ M 6 " -0.003 2.00e-02 2.50e+03 pdb=" C11 PXZ M 6 " 0.029 2.00e-02 2.50e+03 pdb=" C12 PXZ M 6 " 0.025 2.00e-02 2.50e+03 pdb=" C13 PXZ M 6 " 0.020 2.00e-02 2.50e+03 pdb=" C14 PXZ M 6 " 0.010 2.00e-02 2.50e+03 pdb=" C15 PXZ M 6 " 0.010 2.00e-02 2.50e+03 pdb=" C16 PXZ M 6 " -0.013 2.00e-02 2.50e+03 pdb=" C2 PXZ M 6 " -0.018 2.00e-02 2.50e+03 pdb=" C3 PXZ M 6 " -0.017 2.00e-02 2.50e+03 pdb=" C4 PXZ M 6 " 0.015 2.00e-02 2.50e+03 pdb=" C6 PXZ M 6 " -0.009 2.00e-02 2.50e+03 pdb=" C7 PXZ M 6 " -0.029 2.00e-02 2.50e+03 pdb=" C8 PXZ M 6 " -0.043 2.00e-02 2.50e+03 pdb=" C9 PXZ M 6 " -0.020 2.00e-02 2.50e+03 pdb=" N10 PXZ M 6 " 0.054 2.00e-02 2.50e+03 pdb=" N2 PXZ M 6 " -0.037 2.00e-02 2.50e+03 pdb=" O3 PXZ M 6 " -0.039 2.00e-02 2.50e+03 pdb=" O5 PXZ M 6 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " -0.045 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO A 245 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR M 7 " -0.013 2.00e-02 2.50e+03 2.42e-02 5.88e+00 pdb=" C THR M 7 " 0.042 2.00e-02 2.50e+03 pdb=" O THR M 7 " -0.015 2.00e-02 2.50e+03 pdb=" N DVA M 8 " -0.014 2.00e-02 2.50e+03 ... (remaining 5721 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 338 2.58 - 3.16: 27721 3.16 - 3.74: 53228 3.74 - 4.32: 75093 4.32 - 4.90: 123684 Nonbonded interactions: 280064 Sorted by model distance: nonbonded pdb=" O3' C P 12 " pdb="MG MG A1803 " model vdw 1.999 2.170 nonbonded pdb=" NH2 ARG A 469 " pdb=" O GLY B 991 " model vdw 2.111 3.120 nonbonded pdb=" OD1 ASP A 485 " pdb=" O2' C P 12 " model vdw 2.113 3.040 nonbonded pdb=" OG1 THR B 487 " pdb=" O ALA B 777 " model vdw 2.122 3.040 nonbonded pdb=" OD2 ASP E 25 " pdb=" OH TYR E 187 " model vdw 2.138 3.040 ... (remaining 280059 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.020 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 33698 Z= 0.231 Angle : 0.582 9.810 45751 Z= 0.343 Chirality : 0.044 0.253 5140 Planarity : 0.004 0.068 5723 Dihedral : 14.832 157.901 12996 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % 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: 0.37 (0.14), residues: 3936 helix: 0.92 (0.14), residues: 1355 sheet: -0.32 (0.20), residues: 613 loop : 0.10 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 47 TYR 0.020 0.001 TYR B1092 PHE 0.031 0.002 PHE H 118 TRP 0.014 0.001 TRP A 139 HIS 0.006 0.001 HIS A1140 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.23 (33661) covalent geometry : angle 0.56931 / 0.34 (45703) hydrogen bonds : bond 0.13366 / 8.80 ( 1436) hydrogen bonds : angle 6.09105 / 4.40 ( 4006) metal coordination : bond 0.00615 / 0.35 ( 32) metal coordination : angle 3.95494 / 2.70 ( 45) Misc. bond : bond 0.00616 / 0.31 ( 4) link_TRANS : bond 0.00106 / 0.06 ( 1) link_TRANS : angle 0.48244 / 0.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 767 time to evaluate : 1.084 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: A 72 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7039 (mm-30) REVERT: A 124 GLN cc_start: 0.8356 (mt0) cc_final: 0.8078 (mm-40) REVERT: A 247 ARG cc_start: 0.7674 (ptt90) cc_final: 0.7374 (ptt-90) REVERT: A 270 LEU cc_start: 0.7271 (mt) cc_final: 0.6916 (mt) REVERT: A 277 GLU cc_start: 0.7595 (tt0) cc_final: 0.6933 (pt0) REVERT: A 289 ILE cc_start: 0.8059 (mm) cc_final: 0.7817 (pt) REVERT: A 386 ASP cc_start: 0.8218 (m-30) cc_final: 0.7542 (t0) REVERT: A 476 SER cc_start: 0.8942 (t) cc_final: 0.8698 (p) REVERT: A 481 ASP cc_start: 0.7966 (m-30) cc_final: 0.7730 (m-30) REVERT: A 542 GLU cc_start: 0.8244 (mt-10) cc_final: 0.8011 (mp0) REVERT: A 589 GLN cc_start: 0.8835 (tt0) cc_final: 0.8511 (tm-30) REVERT: A 624 SER cc_start: 0.9221 (p) cc_final: 0.8861 (m) REVERT: A 676 MET cc_start: 0.7429 (mmm) cc_final: 0.7116 (mmt) REVERT: A 701 LEU cc_start: 0.8394 (mt) cc_final: 0.7958 (mm) REVERT: A 739 ASP cc_start: 0.8516 (m-30) cc_final: 0.8176 (m-30) REVERT: A 748 MET cc_start: 0.8907 (mtm) cc_final: 0.8667 (mtp) REVERT: A 951 GLU cc_start: 0.7900 (tp30) cc_final: 0.7389 (tp30) REVERT: A 992 ASP cc_start: 0.7531 (m-30) cc_final: 0.7192 (t0) REVERT: A 1034 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7310 (mt-10) REVERT: A 1112 LYS cc_start: 0.8835 (mmpt) cc_final: 0.8080 (mttp) REVERT: A 1209 MET cc_start: 0.7017 (mmm) cc_final: 0.6663 (mtp) REVERT: A 1290 LYS cc_start: 0.7084 (mmmt) cc_final: 0.6837 (mttt) REVERT: A 1297 GLU cc_start: 0.7104 (mp0) cc_final: 0.6894 (mp0) REVERT: A 1312 ASN cc_start: 0.7914 (t0) cc_final: 0.7463 (t0) REVERT: A 1404 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7799 (mt-10) REVERT: A 1411 GLU cc_start: 0.8148 (tp30) cc_final: 0.7730 (tt0) REVERT: A 1454 MET cc_start: 0.6673 (pmm) cc_final: 0.5778 (pmm) REVERT: B 96 TYR cc_start: 0.7789 (m-10) cc_final: 0.7449 (m-10) REVERT: B 103 ASN cc_start: 0.6796 (m-40) cc_final: 0.6429 (p0) REVERT: B 131 ASP cc_start: 0.8982 (m-30) cc_final: 0.8348 (m-30) REVERT: B 177 LYS cc_start: 0.8686 (ttmm) cc_final: 0.8348 (mtmt) REVERT: B 195 CYS cc_start: 0.7830 (t) cc_final: 0.7388 (t) REVERT: B 315 LYS cc_start: 0.4492 (mmtt) cc_final: 0.3269 (ptmm) REVERT: B 319 GLU cc_start: 0.6536 (mm-30) cc_final: 0.6019 (mp0) REVERT: B 353 LYS cc_start: 0.7668 (mtpp) cc_final: 0.7063 (mmtm) REVERT: B 357 GLN cc_start: 0.7522 (tt0) cc_final: 0.7199 (tm-30) REVERT: B 426 LYS cc_start: 0.6914 (ttpt) cc_final: 0.6629 (tppt) REVERT: B 458 LYS cc_start: 0.8026 (mtpt) cc_final: 0.7323 (mttp) REVERT: B 557 PHE cc_start: 0.7879 (m-80) cc_final: 0.7526 (m-80) REVERT: B 622 LYS cc_start: 0.7079 (mtmm) cc_final: 0.6601 (mmpt) REVERT: B 665 GLU cc_start: 0.8116 (tt0) cc_final: 0.7853 (tp30) REVERT: B 811 TYR cc_start: 0.7818 (m-80) cc_final: 0.7127 (m-80) REVERT: B 864 LYS cc_start: 0.7448 (ptpp) cc_final: 0.6138 (mmtp) REVERT: B 868 MET cc_start: 0.6652 (mpp) cc_final: 0.6137 (pmm) REVERT: B 962 LYS cc_start: 0.6848 (ttmt) cc_final: 0.6308 (tttt) REVERT: B 1116 ARG cc_start: 0.7318 (mtt180) cc_final: 0.7090 (mtt-85) REVERT: B 1183 LYS cc_start: 0.7947 (tttt) cc_final: 0.7422 (ttpt) REVERT: C 57 VAL cc_start: 0.8387 (m) cc_final: 0.8154 (p) REVERT: C 94 LYS cc_start: 0.7170 (mtpt) cc_final: 0.6375 (ptpp) REVERT: C 118 LEU cc_start: 0.8001 (mt) cc_final: 0.7759 (mp) REVERT: C 177 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6721 (mp0) REVERT: D 145 MET cc_start: 0.4979 (tpt) cc_final: 0.4008 (mtt) REVERT: E 154 ILE cc_start: 0.8488 (mm) cc_final: 0.8267 (pt) REVERT: E 172 GLU cc_start: 0.8063 (tp30) cc_final: 0.7689 (mm-30) REVERT: E 192 ARG cc_start: 0.7971 (ptm-80) cc_final: 0.7607 (ttp80) REVERT: G 41 LYS cc_start: 0.4959 (tptp) cc_final: 0.4497 (ttpt) REVERT: G 73 LYS cc_start: 0.7150 (mtmt) cc_final: 0.6778 (mtmt) REVERT: H 11 GLN cc_start: 0.7979 (tt0) cc_final: 0.7758 (tm-30) REVERT: H 31 THR cc_start: 0.7846 (t) cc_final: 0.7454 (p) REVERT: H 33 GLN cc_start: 0.7680 (mp10) cc_final: 0.7154 (mp-120) REVERT: H 53 ASP cc_start: 0.8163 (t0) cc_final: 0.7908 (t0) REVERT: H 128 ASN cc_start: 0.8227 (p0) cc_final: 0.8000 (p0) REVERT: I 13 MET cc_start: 0.6072 (ppp) cc_final: 0.5761 (pp-130) REVERT: I 30 ARG cc_start: 0.6203 (mtp180) cc_final: 0.5011 (mmp80) REVERT: I 110 PHE cc_start: 0.7720 (p90) cc_final: 0.7475 (p90) REVERT: J 23 ASN cc_start: 0.7884 (t0) cc_final: 0.7470 (m110) REVERT: J 42 LYS cc_start: 0.8081 (ptmt) cc_final: 0.7676 (ptpt) REVERT: K 37 LYS cc_start: 0.7764 (mmtm) cc_final: 0.7530 (mmtt) REVERT: K 53 ASP cc_start: 0.8337 (t0) cc_final: 0.8104 (t0) REVERT: K 55 LYS cc_start: 0.8318 (mtmt) cc_final: 0.7979 (mtpt) REVERT: K 108 GLU cc_start: 0.7548 (tp30) cc_final: 0.7251 (tp30) outliers start: 0 outliers final: 2 residues processed: 767 average time/residue: 0.6090 time to fit residues: 556.9750 Evaluate side-chains 471 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 469 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 236 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN A 435 HIS A 698 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 HIS B 350 GLN B 518 HIS B 583 ASN B 761 HIS ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN D 28 GLN E 3 GLN F 104 ASN G 14 HIS I 87 GLN I 90 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.174408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.126744 restraints weight = 49036.063| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.77 r_work: 0.3621 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 33698 Z= 0.207 Angle : 0.668 12.790 45751 Z= 0.340 Chirality : 0.046 0.214 5140 Planarity : 0.005 0.072 5723 Dihedral : 12.979 149.238 5026 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.88 % Allowed : 11.00 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % 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: 0.29 (0.13), residues: 3936 helix: 0.83 (0.14), residues: 1369 sheet: -0.40 (0.19), residues: 661 loop : 0.10 (0.15), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 135 TYR 0.018 0.002 TYR H 115 PHE 0.023 0.002 PHE A 219 TRP 0.011 0.001 TRP C 170 HIS 0.011 0.001 HIS G 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (33661) covalent geometry : angle 0.64655 / 0.34 (45703) hydrogen bonds : bond 0.04584 / 3.07 ( 1436) hydrogen bonds : angle 5.11949 / 3.68 ( 4006) metal coordination : bond 0.01252 / 0.76 ( 32) metal coordination : angle 5.35312 / 3.75 ( 45) Misc. bond : bond 0.00084 / 0.04 ( 4) link_TRANS : bond 0.00078 / 0.04 ( 1) link_TRANS : angle 0.49884 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 505 time to evaluate : 1.130 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: A 72 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7089 (mm-30) REVERT: A 124 GLN cc_start: 0.8440 (mt0) cc_final: 0.8140 (mm-40) REVERT: A 133 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8407 (tppp) REVERT: A 175 ARG cc_start: 0.7427 (ttp-110) cc_final: 0.7203 (ptt90) REVERT: A 247 ARG cc_start: 0.7689 (ptt90) cc_final: 0.7324 (ptt-90) REVERT: A 270 LEU cc_start: 0.7223 (mt) cc_final: 0.6974 (mt) REVERT: A 277 GLU cc_start: 0.7641 (tt0) cc_final: 0.6918 (pt0) REVERT: A 330 LYS cc_start: 0.8173 (pttp) cc_final: 0.7845 (ptmt) REVERT: A 373 THR cc_start: 0.8041 (m) cc_final: 0.7641 (p) REVERT: A 386 ASP cc_start: 0.8386 (m-30) cc_final: 0.7727 (t0) REVERT: A 390 GLN cc_start: 0.7622 (tp-100) cc_final: 0.7105 (tp-100) REVERT: A 456 MET cc_start: 0.9021 (mtp) cc_final: 0.8708 (mtm) REVERT: A 476 SER cc_start: 0.8919 (t) cc_final: 0.8705 (p) REVERT: A 542 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7957 (mp0) REVERT: A 589 GLN cc_start: 0.8912 (tt0) cc_final: 0.8591 (tm-30) REVERT: A 644 LYS cc_start: 0.7991 (mmmt) cc_final: 0.7506 (mttp) REVERT: A 678 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7126 (tm-30) REVERT: A 696 GLU cc_start: 0.7445 (tp30) cc_final: 0.6989 (tp30) REVERT: A 720 ARG cc_start: 0.6979 (ttp-170) cc_final: 0.6699 (ttp80) REVERT: A 949 ASP cc_start: 0.8055 (p0) cc_final: 0.7421 (m-30) REVERT: A 951 GLU cc_start: 0.7885 (tp30) cc_final: 0.7172 (tp30) REVERT: A 992 ASP cc_start: 0.7491 (m-30) cc_final: 0.7106 (t0) REVERT: A 1034 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7142 (mt-10) REVERT: A 1112 LYS cc_start: 0.8883 (mmpt) cc_final: 0.8172 (mttp) REVERT: A 1191 TRP cc_start: 0.6647 (m-90) cc_final: 0.6220 (m-90) REVERT: A 1285 MET cc_start: 0.6152 (ttm) cc_final: 0.5379 (ppp) REVERT: A 1290 LYS cc_start: 0.7117 (mmmt) cc_final: 0.6684 (mttt) REVERT: A 1312 ASN cc_start: 0.8109 (t0) cc_final: 0.7425 (t0) REVERT: A 1411 GLU cc_start: 0.8217 (tp30) cc_final: 0.7761 (tt0) REVERT: A 1454 MET cc_start: 0.6749 (pmm) cc_final: 0.5839 (pmm) REVERT: B 69 LEU cc_start: 0.8478 (mt) cc_final: 0.8199 (mp) REVERT: B 96 TYR cc_start: 0.7701 (m-10) cc_final: 0.7338 (m-10) REVERT: B 103 ASN cc_start: 0.6800 (m-40) cc_final: 0.6191 (p0) REVERT: B 131 ASP cc_start: 0.8953 (m-30) cc_final: 0.8259 (m-30) REVERT: B 164 LYS cc_start: 0.8227 (pptt) cc_final: 0.7852 (pttp) REVERT: B 177 LYS cc_start: 0.8730 (ttmm) cc_final: 0.8294 (mptt) REVERT: B 195 CYS cc_start: 0.7630 (t) cc_final: 0.7222 (t) REVERT: B 236 HIS cc_start: 0.8226 (m90) cc_final: 0.7994 (m90) REVERT: B 258 LEU cc_start: 0.7961 (tt) cc_final: 0.7710 (tt) REVERT: B 270 LYS cc_start: 0.7484 (mttt) cc_final: 0.7187 (mttm) REVERT: B 309 GLN cc_start: 0.7919 (mt0) cc_final: 0.7572 (mp10) REVERT: B 315 LYS cc_start: 0.4459 (mmtt) cc_final: 0.3341 (ptmm) REVERT: B 319 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6531 (mp0) REVERT: B 353 LYS cc_start: 0.7863 (mtpp) cc_final: 0.7244 (mmtm) REVERT: B 357 GLN cc_start: 0.7373 (tt0) cc_final: 0.7115 (tm-30) REVERT: B 426 LYS cc_start: 0.6879 (ttpt) cc_final: 0.6500 (mptt) REVERT: B 458 LYS cc_start: 0.8005 (mtpt) cc_final: 0.7351 (mttp) REVERT: B 561 TRP cc_start: 0.7721 (m100) cc_final: 0.7391 (m100) REVERT: B 564 GLU cc_start: 0.7824 (tt0) cc_final: 0.7573 (tt0) REVERT: B 622 LYS cc_start: 0.7244 (mtmm) cc_final: 0.6794 (mmpt) REVERT: B 665 GLU cc_start: 0.8116 (tt0) cc_final: 0.7893 (tp30) REVERT: B 789 MET cc_start: 0.8056 (mmt) cc_final: 0.7562 (mmm) REVERT: B 809 MET cc_start: 0.8450 (ptp) cc_final: 0.8154 (ptp) REVERT: B 864 LYS cc_start: 0.7490 (ptpp) cc_final: 0.6348 (tttt) REVERT: B 868 MET cc_start: 0.6722 (mpp) cc_final: 0.6341 (pmm) REVERT: B 1116 ARG cc_start: 0.7244 (mtt180) cc_final: 0.7015 (mtt-85) REVERT: B 1183 LYS cc_start: 0.8044 (tttt) cc_final: 0.7614 (ttpt) REVERT: C 50 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7168 (mm-30) REVERT: C 57 VAL cc_start: 0.8402 (m) cc_final: 0.8081 (p) REVERT: C 94 LYS cc_start: 0.7153 (mtpt) cc_final: 0.6393 (ptpp) REVERT: C 166 GLU cc_start: 0.7888 (tp30) cc_final: 0.7683 (tp30) REVERT: C 177 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6536 (mp0) REVERT: C 205 LYS cc_start: 0.8224 (pttp) cc_final: 0.7798 (mptt) REVERT: C 253 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7378 (mtmm) REVERT: D 145 MET cc_start: 0.4152 (tpt) cc_final: 0.3717 (mtt) REVERT: E 57 MET cc_start: 0.7811 (tmm) cc_final: 0.7041 (ptt) REVERT: E 133 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7788 (mt-10) REVERT: E 154 ILE cc_start: 0.8443 (mm) cc_final: 0.8153 (pt) REVERT: E 172 GLU cc_start: 0.8344 (tp30) cc_final: 0.7891 (mm-30) REVERT: E 192 ARG cc_start: 0.8147 (ptm-80) cc_final: 0.7679 (ttp80) REVERT: F 122 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.6994 (mtt) REVERT: F 123 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7342 (ttpt) REVERT: G 33 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7044 (tt0) REVERT: G 41 LYS cc_start: 0.4218 (tptp) cc_final: 0.3615 (ttpt) REVERT: G 73 LYS cc_start: 0.5617 (mtmt) cc_final: 0.5149 (mtmt) REVERT: H 11 GLN cc_start: 0.7991 (tt0) cc_final: 0.7197 (tm-30) REVERT: H 27 GLU cc_start: 0.8147 (mp0) cc_final: 0.7909 (mp0) REVERT: H 31 THR cc_start: 0.7909 (t) cc_final: 0.7458 (p) REVERT: H 33 GLN cc_start: 0.7532 (mp10) cc_final: 0.6938 (mp10) REVERT: H 52 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7170 (mm-40) REVERT: H 87 ARG cc_start: 0.8159 (mtp85) cc_final: 0.7886 (mtp85) REVERT: H 128 ASN cc_start: 0.8228 (p0) cc_final: 0.7878 (p0) REVERT: I 110 PHE cc_start: 0.7551 (p90) cc_final: 0.7257 (p90) REVERT: J 23 ASN cc_start: 0.7717 (t0) cc_final: 0.7135 (m110) REVERT: J 42 LYS cc_start: 0.8203 (ptmt) cc_final: 0.7610 (ptpt) REVERT: K 37 LYS cc_start: 0.7751 (mmtm) cc_final: 0.7488 (mmtt) REVERT: K 55 LYS cc_start: 0.8099 (mtmt) cc_final: 0.7785 (mtpt) REVERT: K 72 LYS cc_start: 0.8715 (mmmm) cc_final: 0.8448 (mttt) REVERT: K 108 GLU cc_start: 0.7500 (tp30) cc_final: 0.7247 (tp30) REVERT: L 33 GLU cc_start: 0.7936 (tp30) cc_final: 0.7622 (tt0) outliers start: 101 outliers final: 46 residues processed: 557 average time/residue: 0.6297 time to fit residues: 417.1574 Evaluate side-chains 482 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 431 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1168 LEU Chi-restraints excluded: chain B residue 1178 ASN Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1221 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 108 optimal weight: 4.9990 chunk 342 optimal weight: 5.9990 chunk 370 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 212 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 311 optimal weight: 0.9990 chunk 295 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN A1124 HIS ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN B1178 ASN F 104 ASN G 14 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.174947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.127881 restraints weight = 48811.730| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.75 r_work: 0.3635 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 33698 Z= 0.158 Angle : 0.623 18.183 45751 Z= 0.315 Chirality : 0.044 0.207 5140 Planarity : 0.004 0.073 5723 Dihedral : 12.957 146.726 5022 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.88 % Rotamer: Outliers : 2.88 % Allowed : 13.31 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.13), residues: 3936 helix: 0.89 (0.14), residues: 1368 sheet: -0.30 (0.20), residues: 661 loop : 0.09 (0.15), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 135 TYR 0.026 0.002 TYR B1092 PHE 0.025 0.002 PHE A 219 TRP 0.008 0.001 TRP C 201 HIS 0.007 0.001 HIS G 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (33661) covalent geometry : angle 0.59576 / 0.31 (45703) hydrogen bonds : bond 0.04061 / 2.71 ( 1436) hydrogen bonds : angle 4.88118 / 3.51 ( 4006) metal coordination : bond 0.01366 / 0.70 ( 32) metal coordination : angle 5.89043 / 4.00 ( 45) Misc. bond : bond 0.00097 / 0.05 ( 4) link_TRANS : bond 0.00000 / 0.00 ( 1) link_TRANS : angle 0.31471 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 462 time to evaluate : 0.880 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: A 72 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7043 (mm-30) REVERT: A 74 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.6278 (mmt) REVERT: A 123 ARG cc_start: 0.7345 (mtm180) cc_final: 0.6876 (mtm180) REVERT: A 124 GLN cc_start: 0.8466 (mt0) cc_final: 0.8153 (mm-40) REVERT: A 133 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8349 (tppp) REVERT: A 157 ASP cc_start: 0.5862 (p0) cc_final: 0.5625 (p0) REVERT: A 175 ARG cc_start: 0.7388 (ttp-110) cc_final: 0.7181 (ptt90) REVERT: A 247 ARG cc_start: 0.7670 (ptt90) cc_final: 0.7263 (ptt-90) REVERT: A 277 GLU cc_start: 0.7617 (tt0) cc_final: 0.6833 (pt0) REVERT: A 330 LYS cc_start: 0.8134 (pttp) cc_final: 0.7776 (ptmt) REVERT: A 373 THR cc_start: 0.8083 (m) cc_final: 0.7750 (p) REVERT: A 386 ASP cc_start: 0.8392 (m-30) cc_final: 0.7784 (t0) REVERT: A 390 GLN cc_start: 0.7626 (tp-100) cc_final: 0.6937 (tp-100) REVERT: A 476 SER cc_start: 0.8904 (t) cc_final: 0.8684 (p) REVERT: A 542 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7838 (mp0) REVERT: A 589 GLN cc_start: 0.8864 (tt0) cc_final: 0.8541 (tm-30) REVERT: A 644 LYS cc_start: 0.7923 (mmmt) cc_final: 0.7468 (mttm) REVERT: A 678 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7041 (tm-30) REVERT: A 696 GLU cc_start: 0.7438 (tp30) cc_final: 0.7013 (tp30) REVERT: A 720 ARG cc_start: 0.6979 (ttp-170) cc_final: 0.6654 (ttp80) REVERT: A 949 ASP cc_start: 0.8089 (p0) cc_final: 0.7459 (m-30) REVERT: A 951 GLU cc_start: 0.7840 (tp30) cc_final: 0.7139 (tp30) REVERT: A 992 ASP cc_start: 0.7492 (m-30) cc_final: 0.7093 (t0) REVERT: A 1074 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: A 1112 LYS cc_start: 0.8922 (mmpt) cc_final: 0.8177 (mttp) REVERT: A 1191 TRP cc_start: 0.6587 (m-90) cc_final: 0.6183 (m-90) REVERT: A 1290 LYS cc_start: 0.7190 (mmmt) cc_final: 0.6756 (mttt) REVERT: A 1312 ASN cc_start: 0.8158 (t0) cc_final: 0.7460 (t0) REVERT: A 1454 MET cc_start: 0.6625 (pmm) cc_final: 0.5651 (pmm) REVERT: B 96 TYR cc_start: 0.7697 (m-80) cc_final: 0.7218 (m-10) REVERT: B 103 ASN cc_start: 0.6762 (m-40) cc_final: 0.6179 (p0) REVERT: B 131 ASP cc_start: 0.8941 (m-30) cc_final: 0.8486 (m-30) REVERT: B 164 LYS cc_start: 0.8182 (pptt) cc_final: 0.7813 (pttp) REVERT: B 177 LYS cc_start: 0.8753 (ttmm) cc_final: 0.8445 (mptt) REVERT: B 258 LEU cc_start: 0.7954 (tt) cc_final: 0.7745 (tt) REVERT: B 270 LYS cc_start: 0.7541 (mttt) cc_final: 0.7245 (mttm) REVERT: B 309 GLN cc_start: 0.7933 (mt0) cc_final: 0.7661 (mp10) REVERT: B 315 LYS cc_start: 0.4570 (mmtt) cc_final: 0.3553 (ptmm) REVERT: B 353 LYS cc_start: 0.8034 (mtpp) cc_final: 0.7606 (mtpp) REVERT: B 357 GLN cc_start: 0.7360 (tt0) cc_final: 0.7084 (tm-30) REVERT: B 426 LYS cc_start: 0.6842 (ttpt) cc_final: 0.6639 (tppt) REVERT: B 458 LYS cc_start: 0.7964 (mtpt) cc_final: 0.7303 (mttp) REVERT: B 561 TRP cc_start: 0.7654 (m100) cc_final: 0.7445 (m100) REVERT: B 564 GLU cc_start: 0.8026 (tt0) cc_final: 0.7603 (tt0) REVERT: B 615 MET cc_start: 0.7898 (mtt) cc_final: 0.7684 (mtt) REVERT: B 622 LYS cc_start: 0.7246 (mtmm) cc_final: 0.6807 (mmpt) REVERT: B 809 MET cc_start: 0.8354 (ptp) cc_final: 0.8087 (ptp) REVERT: B 860 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7624 (tmm) REVERT: B 864 LYS cc_start: 0.7495 (ptpp) cc_final: 0.6134 (mttt) REVERT: B 868 MET cc_start: 0.6845 (mpp) cc_final: 0.6105 (pmm) REVERT: B 1009 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7768 (m-30) REVERT: B 1178 ASN cc_start: 0.8050 (m-40) cc_final: 0.7801 (t0) REVERT: B 1183 LYS cc_start: 0.7888 (tttt) cc_final: 0.7137 (ttpt) REVERT: C 50 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7145 (mm-30) REVERT: C 57 VAL cc_start: 0.8291 (m) cc_final: 0.7949 (p) REVERT: C 94 LYS cc_start: 0.7119 (mtpt) cc_final: 0.6358 (ptpp) REVERT: C 166 GLU cc_start: 0.7920 (tp30) cc_final: 0.7711 (tp30) REVERT: C 177 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6545 (mp0) REVERT: C 205 LYS cc_start: 0.8317 (pttp) cc_final: 0.7874 (mptt) REVERT: D 29 LEU cc_start: 0.5020 (mm) cc_final: 0.4801 (tp) REVERT: D 61 GLU cc_start: 0.7051 (pp20) cc_final: 0.6788 (pt0) REVERT: D 145 MET cc_start: 0.4119 (tpt) cc_final: 0.3645 (mtt) REVERT: E 57 MET cc_start: 0.7782 (tmm) cc_final: 0.7576 (tpp) REVERT: E 154 ILE cc_start: 0.8436 (mm) cc_final: 0.8187 (pt) REVERT: E 172 GLU cc_start: 0.8283 (tp30) cc_final: 0.7897 (mm-30) REVERT: E 192 ARG cc_start: 0.8111 (ptm-80) cc_final: 0.7649 (ttp80) REVERT: G 33 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7028 (tt0) REVERT: G 41 LYS cc_start: 0.4250 (tptp) cc_final: 0.3627 (ttpt) REVERT: G 73 LYS cc_start: 0.5764 (mtmt) cc_final: 0.5242 (mtmt) REVERT: H 11 GLN cc_start: 0.7983 (tt0) cc_final: 0.7187 (tm-30) REVERT: H 27 GLU cc_start: 0.8113 (mp0) cc_final: 0.7801 (mp0) REVERT: H 31 THR cc_start: 0.7894 (t) cc_final: 0.7448 (p) REVERT: H 33 GLN cc_start: 0.7520 (mp10) cc_final: 0.6876 (mp-120) REVERT: H 52 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7222 (mm-40) REVERT: H 87 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7974 (mtp85) REVERT: I 101 PHE cc_start: 0.6878 (m-10) cc_final: 0.6592 (m-10) REVERT: I 110 PHE cc_start: 0.7550 (p90) cc_final: 0.7160 (p90) REVERT: J 23 ASN cc_start: 0.7732 (t0) cc_final: 0.7140 (m110) REVERT: J 42 LYS cc_start: 0.8217 (ptmt) cc_final: 0.7615 (ptpt) REVERT: K 35 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.8259 (m-80) REVERT: K 37 LYS cc_start: 0.7752 (mmtm) cc_final: 0.7479 (mmtt) REVERT: K 72 LYS cc_start: 0.8714 (mmmm) cc_final: 0.8477 (mttt) REVERT: K 108 GLU cc_start: 0.7441 (tp30) cc_final: 0.7218 (tp30) REVERT: L 33 GLU cc_start: 0.7928 (tp30) cc_final: 0.7664 (tt0) outliers start: 101 outliers final: 39 residues processed: 519 average time/residue: 0.6232 time to fit residues: 385.3789 Evaluate side-chains 463 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 417 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1221 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 35 PHE Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 51 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 198 optimal weight: 7.9990 chunk 363 optimal weight: 0.0470 chunk 106 optimal weight: 0.0770 chunk 162 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 217 optimal weight: 1.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 HIS C 214 ASN E 104 ASN F 104 ASN G 102 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.174558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.127343 restraints weight = 48832.051| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.76 r_work: 0.3620 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 33698 Z= 0.152 Angle : 0.597 18.744 45751 Z= 0.303 Chirality : 0.044 0.205 5140 Planarity : 0.004 0.074 5723 Dihedral : 12.930 145.743 5022 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.94 % Allowed : 14.77 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.14), residues: 3936 helix: 0.95 (0.14), residues: 1370 sheet: -0.32 (0.20), residues: 647 loop : 0.08 (0.15), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 130 TYR 0.015 0.001 TYR B 811 PHE 0.025 0.002 PHE A 219 TRP 0.010 0.001 TRP E 13 HIS 0.005 0.001 HIS A1140 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (33661) covalent geometry : angle 0.57276 / 0.30 (45703) hydrogen bonds : bond 0.03814 / 2.57 ( 1436) hydrogen bonds : angle 4.76370 / 3.43 ( 4006) metal coordination : bond 0.00773 / 0.44 ( 32) metal coordination : angle 5.36204 / 3.51 ( 45) Misc. bond : bond 0.00072 / 0.03 ( 4) link_TRANS : bond 0.00011 / 0.01 ( 1) link_TRANS : angle 0.28761 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 447 time to evaluate : 1.216 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: A 72 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6875 (mm-30) REVERT: A 74 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6602 (mmt) REVERT: A 123 ARG cc_start: 0.7392 (mtm180) cc_final: 0.7023 (mtm180) REVERT: A 124 GLN cc_start: 0.8457 (mt0) cc_final: 0.8145 (mm-40) REVERT: A 133 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8350 (tppp) REVERT: A 157 ASP cc_start: 0.5980 (p0) cc_final: 0.5768 (p0) REVERT: A 175 ARG cc_start: 0.7436 (ttp-110) cc_final: 0.7200 (ptt90) REVERT: A 247 ARG cc_start: 0.7674 (ptt90) cc_final: 0.7246 (ptt-90) REVERT: A 277 GLU cc_start: 0.7663 (tt0) cc_final: 0.6833 (pt0) REVERT: A 330 LYS cc_start: 0.8119 (pttp) cc_final: 0.7757 (ptmt) REVERT: A 373 THR cc_start: 0.8088 (m) cc_final: 0.7793 (p) REVERT: A 386 ASP cc_start: 0.8421 (m-30) cc_final: 0.7805 (t0) REVERT: A 390 GLN cc_start: 0.7644 (tp-100) cc_final: 0.7116 (tp-100) REVERT: A 415 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7833 (mm) REVERT: A 456 MET cc_start: 0.8962 (mtp) cc_final: 0.8618 (mtm) REVERT: A 476 SER cc_start: 0.8925 (t) cc_final: 0.8703 (p) REVERT: A 542 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7832 (mp0) REVERT: A 589 GLN cc_start: 0.8857 (tt0) cc_final: 0.8529 (tm-30) REVERT: A 592 ASP cc_start: 0.8371 (m-30) cc_final: 0.8142 (m-30) REVERT: A 624 SER cc_start: 0.8978 (p) cc_final: 0.8549 (m) REVERT: A 644 LYS cc_start: 0.7973 (mmmt) cc_final: 0.7499 (mttp) REVERT: A 678 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7052 (tm-30) REVERT: A 688 LYS cc_start: 0.8073 (mmtp) cc_final: 0.7467 (tmtt) REVERT: A 696 GLU cc_start: 0.7422 (tp30) cc_final: 0.6879 (tp30) REVERT: A 720 ARG cc_start: 0.6976 (ttp-170) cc_final: 0.6604 (ttp80) REVERT: A 755 PHE cc_start: 0.7830 (t80) cc_final: 0.7588 (t80) REVERT: A 833 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6998 (tp30) REVERT: A 949 ASP cc_start: 0.8097 (p0) cc_final: 0.7504 (m-30) REVERT: A 951 GLU cc_start: 0.7859 (tp30) cc_final: 0.7149 (tp30) REVERT: A 992 ASP cc_start: 0.7500 (m-30) cc_final: 0.7107 (t0) REVERT: A 1034 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6532 (mt-10) REVERT: A 1074 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7744 (tt0) REVERT: A 1112 LYS cc_start: 0.8984 (mmpt) cc_final: 0.8191 (mttp) REVERT: A 1191 TRP cc_start: 0.6597 (m-90) cc_final: 0.6200 (m-90) REVERT: A 1285 MET cc_start: 0.5634 (OUTLIER) cc_final: 0.5359 (ttp) REVERT: A 1290 LYS cc_start: 0.7189 (mmmt) cc_final: 0.6742 (mttt) REVERT: A 1312 ASN cc_start: 0.8153 (t0) cc_final: 0.7434 (t0) REVERT: A 1454 MET cc_start: 0.6667 (pmm) cc_final: 0.5634 (pmm) REVERT: B 96 TYR cc_start: 0.7500 (m-80) cc_final: 0.7009 (m-10) REVERT: B 103 ASN cc_start: 0.6775 (m-40) cc_final: 0.6229 (p0) REVERT: B 131 ASP cc_start: 0.8924 (m-30) cc_final: 0.8223 (m-30) REVERT: B 177 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8507 (mptt) REVERT: B 258 LEU cc_start: 0.7937 (tt) cc_final: 0.7737 (tt) REVERT: B 270 LYS cc_start: 0.7524 (mttt) cc_final: 0.7229 (mttm) REVERT: B 309 GLN cc_start: 0.7940 (mt0) cc_final: 0.7720 (mp10) REVERT: B 315 LYS cc_start: 0.4321 (mmtt) cc_final: 0.3682 (ptmm) REVERT: B 332 ASP cc_start: 0.7389 (t0) cc_final: 0.7115 (t0) REVERT: B 353 LYS cc_start: 0.8147 (mtpp) cc_final: 0.7706 (mtpp) REVERT: B 357 GLN cc_start: 0.7204 (tt0) cc_final: 0.6990 (tm-30) REVERT: B 398 ARG cc_start: 0.8235 (ttm-80) cc_final: 0.7882 (tpp80) REVERT: B 426 LYS cc_start: 0.6863 (ttpt) cc_final: 0.6641 (mppt) REVERT: B 458 LYS cc_start: 0.7974 (mtpt) cc_final: 0.7315 (mttp) REVERT: B 468 GLU cc_start: 0.5583 (OUTLIER) cc_final: 0.3923 (pt0) REVERT: B 564 GLU cc_start: 0.7993 (tt0) cc_final: 0.7582 (tt0) REVERT: B 617 ARG cc_start: 0.7300 (ttp80) cc_final: 0.7075 (ttp80) REVERT: B 622 LYS cc_start: 0.7274 (mtmm) cc_final: 0.6800 (mmpt) REVERT: B 809 MET cc_start: 0.8304 (ptp) cc_final: 0.7994 (ptp) REVERT: B 864 LYS cc_start: 0.7561 (ptpp) cc_final: 0.6406 (mttt) REVERT: B 904 ARG cc_start: 0.7889 (mtt90) cc_final: 0.7518 (mmt-90) REVERT: B 941 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7338 (tp) REVERT: B 1009 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7746 (m-30) REVERT: B 1183 LYS cc_start: 0.7659 (tttt) cc_final: 0.7390 (ttpt) REVERT: C 50 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7265 (mm-30) REVERT: C 57 VAL cc_start: 0.8285 (m) cc_final: 0.7918 (p) REVERT: C 78 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7183 (tp30) REVERT: C 94 LYS cc_start: 0.7149 (mtpt) cc_final: 0.6429 (ptpp) REVERT: C 135 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7974 (mm-40) REVERT: C 152 GLU cc_start: 0.6956 (pm20) cc_final: 0.6632 (pm20) REVERT: C 177 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6530 (mp0) REVERT: C 205 LYS cc_start: 0.8328 (pttp) cc_final: 0.7873 (mptt) REVERT: D 29 LEU cc_start: 0.5042 (mm) cc_final: 0.4818 (tp) REVERT: D 145 MET cc_start: 0.4037 (tpt) cc_final: 0.3489 (mtt) REVERT: E 45 LYS cc_start: 0.8042 (mmpt) cc_final: 0.7445 (ptpt) REVERT: E 57 MET cc_start: 0.7952 (tmm) cc_final: 0.7439 (tpp) REVERT: E 154 ILE cc_start: 0.8433 (mm) cc_final: 0.8196 (pt) REVERT: E 172 GLU cc_start: 0.8279 (tp30) cc_final: 0.7918 (mm-30) REVERT: E 192 ARG cc_start: 0.8100 (ptm-80) cc_final: 0.7647 (ttp80) REVERT: F 122 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7072 (mtt) REVERT: G 41 LYS cc_start: 0.4280 (tptp) cc_final: 0.3650 (ttpt) REVERT: G 73 LYS cc_start: 0.5687 (mtmt) cc_final: 0.5181 (mtmt) REVERT: H 11 GLN cc_start: 0.7993 (tt0) cc_final: 0.7756 (tt0) REVERT: H 19 ARG cc_start: 0.8856 (mtp85) cc_final: 0.8442 (mtp85) REVERT: H 27 GLU cc_start: 0.8081 (mp0) cc_final: 0.7772 (mp0) REVERT: H 31 THR cc_start: 0.7916 (t) cc_final: 0.7471 (p) REVERT: H 33 GLN cc_start: 0.7504 (mp10) cc_final: 0.6818 (mp-120) REVERT: H 52 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7508 (mm-40) REVERT: H 87 ARG cc_start: 0.8218 (mtp85) cc_final: 0.7996 (mtp85) REVERT: H 138 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6746 (pm20) REVERT: I 101 PHE cc_start: 0.6911 (m-10) cc_final: 0.6603 (m-10) REVERT: I 110 PHE cc_start: 0.7462 (p90) cc_final: 0.7056 (p90) REVERT: J 23 ASN cc_start: 0.7744 (t0) cc_final: 0.7153 (m110) REVERT: J 42 LYS cc_start: 0.8226 (ptmt) cc_final: 0.7603 (ptpt) REVERT: K 35 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8251 (m-80) REVERT: K 37 LYS cc_start: 0.7686 (mmtm) cc_final: 0.7387 (mmtt) REVERT: K 55 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7642 (mtpt) REVERT: K 108 GLU cc_start: 0.7481 (tp30) cc_final: 0.7265 (tp30) REVERT: L 33 GLU cc_start: 0.7941 (tp30) cc_final: 0.7690 (tt0) REVERT: L 62 LYS cc_start: 0.8218 (mmmm) cc_final: 0.7991 (mmtm) outliers start: 103 outliers final: 52 residues processed: 511 average time/residue: 0.6530 time to fit residues: 399.3358 Evaluate side-chains 482 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 416 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1168 LEU Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1221 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 35 PHE Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 51 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 370 optimal weight: 5.9990 chunk 327 optimal weight: 0.9980 chunk 204 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 230 optimal weight: 7.9990 chunk 331 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 355 optimal weight: 7.9990 chunk 31 optimal weight: 0.0980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 ASN ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1178 ASN C 214 ASN F 104 ASN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.173435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.126136 restraints weight = 48883.994| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.75 r_work: 0.3618 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 33698 Z= 0.173 Angle : 0.613 17.094 45751 Z= 0.310 Chirality : 0.044 0.217 5140 Planarity : 0.004 0.074 5723 Dihedral : 12.934 145.760 5022 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.82 % Allowed : 15.99 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % 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: 0.37 (0.14), residues: 3936 helix: 0.95 (0.14), residues: 1372 sheet: -0.37 (0.20), residues: 663 loop : 0.10 (0.15), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 130 TYR 0.024 0.001 TYR I 15 PHE 0.025 0.002 PHE A 219 TRP 0.011 0.001 TRP A 430 HIS 0.006 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (33661) covalent geometry : angle 0.59118 / 0.31 (45703) hydrogen bonds : bond 0.03821 / 2.57 ( 1436) hydrogen bonds : angle 4.77918 / 3.44 ( 4006) metal coordination : bond 0.00763 / 0.43 ( 32) metal coordination : angle 5.19499 / 3.45 ( 45) Misc. bond : bond 0.00055 / 0.03 ( 4) link_TRANS : bond 0.00043 / 0.02 ( 1) link_TRANS : angle 0.23547 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 424 time to evaluate : 1.172 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 57 ARG cc_start: 0.7178 (mtm-85) cc_final: 0.6891 (mtm-85) REVERT: A 72 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6882 (mm-30) REVERT: A 74 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6630 (mmt) REVERT: A 123 ARG cc_start: 0.7432 (mtm180) cc_final: 0.7061 (mtm180) REVERT: A 124 GLN cc_start: 0.8466 (mt0) cc_final: 0.8188 (mm-40) REVERT: A 133 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8353 (tppp) REVERT: A 175 ARG cc_start: 0.7464 (ttp-110) cc_final: 0.7241 (ptt90) REVERT: A 247 ARG cc_start: 0.7716 (ptt90) cc_final: 0.7293 (ptt-90) REVERT: A 277 GLU cc_start: 0.7749 (tt0) cc_final: 0.6898 (pt0) REVERT: A 330 LYS cc_start: 0.8189 (pttp) cc_final: 0.7962 (pttt) REVERT: A 373 THR cc_start: 0.8139 (m) cc_final: 0.7857 (p) REVERT: A 386 ASP cc_start: 0.8354 (m-30) cc_final: 0.7772 (t0) REVERT: A 390 GLN cc_start: 0.7646 (tp-100) cc_final: 0.7109 (tp-100) REVERT: A 415 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7890 (mm) REVERT: A 456 MET cc_start: 0.9027 (mtp) cc_final: 0.8671 (mtm) REVERT: A 476 SER cc_start: 0.8932 (t) cc_final: 0.8713 (p) REVERT: A 495 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8168 (mp0) REVERT: A 542 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7915 (mp0) REVERT: A 589 GLN cc_start: 0.8854 (tt0) cc_final: 0.8540 (tm-30) REVERT: A 592 ASP cc_start: 0.8393 (m-30) cc_final: 0.8142 (m-30) REVERT: A 624 SER cc_start: 0.8970 (p) cc_final: 0.8555 (m) REVERT: A 678 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7155 (tm-30) REVERT: A 688 LYS cc_start: 0.8066 (mmtp) cc_final: 0.7478 (tmtt) REVERT: A 720 ARG cc_start: 0.6990 (ttp-170) cc_final: 0.6623 (ttp80) REVERT: A 755 PHE cc_start: 0.7916 (t80) cc_final: 0.7695 (t80) REVERT: A 833 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7063 (tm-30) REVERT: A 949 ASP cc_start: 0.8077 (p0) cc_final: 0.7568 (m-30) REVERT: A 951 GLU cc_start: 0.7921 (tp30) cc_final: 0.7204 (tp30) REVERT: A 992 ASP cc_start: 0.7535 (m-30) cc_final: 0.7137 (t0) REVERT: A 1112 LYS cc_start: 0.8947 (mmpt) cc_final: 0.8177 (mttp) REVERT: A 1191 TRP cc_start: 0.6736 (m-90) cc_final: 0.6280 (m-90) REVERT: A 1290 LYS cc_start: 0.7270 (mmmt) cc_final: 0.6823 (mttt) REVERT: A 1312 ASN cc_start: 0.8262 (t0) cc_final: 0.7570 (t0) REVERT: A 1454 MET cc_start: 0.6706 (pmm) cc_final: 0.5563 (pmm) REVERT: B 89 GLU cc_start: 0.7772 (pt0) cc_final: 0.6797 (pp20) REVERT: B 96 TYR cc_start: 0.7492 (m-80) cc_final: 0.7024 (m-10) REVERT: B 103 ASN cc_start: 0.6825 (m-40) cc_final: 0.6300 (p0) REVERT: B 131 ASP cc_start: 0.8911 (m-30) cc_final: 0.8307 (m-30) REVERT: B 135 ARG cc_start: 0.6775 (mmm160) cc_final: 0.6228 (mtp180) REVERT: B 177 LYS cc_start: 0.8765 (ttmm) cc_final: 0.8508 (mptt) REVERT: B 270 LYS cc_start: 0.7568 (mttt) cc_final: 0.7260 (mttm) REVERT: B 309 GLN cc_start: 0.7913 (mt0) cc_final: 0.7708 (mp10) REVERT: B 315 LYS cc_start: 0.4477 (mmtt) cc_final: 0.3928 (ptmm) REVERT: B 353 LYS cc_start: 0.8166 (mtpp) cc_final: 0.7704 (mtpp) REVERT: B 357 GLN cc_start: 0.7197 (tt0) cc_final: 0.6981 (tm-30) REVERT: B 398 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7870 (tpp80) REVERT: B 426 LYS cc_start: 0.6887 (ttpt) cc_final: 0.6673 (mppt) REVERT: B 458 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7375 (mttp) REVERT: B 468 GLU cc_start: 0.5676 (OUTLIER) cc_final: 0.3996 (pt0) REVERT: B 564 GLU cc_start: 0.7978 (tt0) cc_final: 0.7554 (tt0) REVERT: B 615 MET cc_start: 0.7848 (mtt) cc_final: 0.7622 (mtt) REVERT: B 617 ARG cc_start: 0.7332 (ttp80) cc_final: 0.7118 (ttp80) REVERT: B 622 LYS cc_start: 0.7485 (mtmm) cc_final: 0.7078 (mmpt) REVERT: B 809 MET cc_start: 0.8341 (ptp) cc_final: 0.8047 (ptp) REVERT: B 860 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7604 (tmm) REVERT: B 864 LYS cc_start: 0.7602 (ptpp) cc_final: 0.6374 (mttt) REVERT: B 904 ARG cc_start: 0.7939 (mtt90) cc_final: 0.7574 (mmt-90) REVERT: B 941 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7360 (tp) REVERT: C 50 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7378 (mm-30) REVERT: C 57 VAL cc_start: 0.8297 (m) cc_final: 0.8034 (p) REVERT: C 78 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7245 (tp30) REVERT: C 94 LYS cc_start: 0.7116 (mtpt) cc_final: 0.6518 (ptpp) REVERT: C 177 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6559 (mp0) REVERT: C 205 LYS cc_start: 0.8368 (pttp) cc_final: 0.7911 (mptt) REVERT: C 214 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8085 (m-40) REVERT: C 253 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7391 (mtmm) REVERT: D 29 LEU cc_start: 0.5102 (mm) cc_final: 0.4836 (tp) REVERT: D 61 GLU cc_start: 0.7010 (pp20) cc_final: 0.6760 (pt0) REVERT: D 145 MET cc_start: 0.4139 (tpt) cc_final: 0.3424 (mtt) REVERT: E 39 LEU cc_start: 0.6890 (tm) cc_final: 0.6667 (tm) REVERT: E 57 MET cc_start: 0.7816 (tmm) cc_final: 0.7234 (tpp) REVERT: E 154 ILE cc_start: 0.8478 (mm) cc_final: 0.8245 (pt) REVERT: E 172 GLU cc_start: 0.8277 (tp30) cc_final: 0.7956 (mm-30) REVERT: E 192 ARG cc_start: 0.8101 (ptm-80) cc_final: 0.7667 (ttp80) REVERT: G 41 LYS cc_start: 0.4330 (tptp) cc_final: 0.3662 (ttpt) REVERT: G 73 LYS cc_start: 0.5830 (mtmt) cc_final: 0.5325 (mtmt) REVERT: H 27 GLU cc_start: 0.8169 (mp0) cc_final: 0.7850 (mp0) REVERT: H 31 THR cc_start: 0.7939 (t) cc_final: 0.7497 (p) REVERT: H 33 GLN cc_start: 0.7574 (mp10) cc_final: 0.6871 (mp-120) REVERT: H 52 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7597 (mm-40) REVERT: H 87 ARG cc_start: 0.8218 (mtp85) cc_final: 0.7999 (mtp85) REVERT: H 138 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6890 (pm20) REVERT: I 101 PHE cc_start: 0.6947 (m-10) cc_final: 0.6645 (m-10) REVERT: I 110 PHE cc_start: 0.7485 (p90) cc_final: 0.7097 (p90) REVERT: J 23 ASN cc_start: 0.7782 (t0) cc_final: 0.7190 (m110) REVERT: J 42 LYS cc_start: 0.8272 (ptmt) cc_final: 0.7657 (ptpt) REVERT: K 35 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8327 (m-80) REVERT: K 37 LYS cc_start: 0.7694 (mmtm) cc_final: 0.7394 (mmtt) REVERT: K 72 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8605 (mttt) REVERT: L 33 GLU cc_start: 0.7950 (tp30) cc_final: 0.7696 (tt0) REVERT: L 62 LYS cc_start: 0.8280 (mmmm) cc_final: 0.8037 (mmtm) outliers start: 99 outliers final: 51 residues processed: 486 average time/residue: 0.6595 time to fit residues: 382.4712 Evaluate side-chains 469 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 407 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1269 GLU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1168 LEU Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1221 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 35 PHE Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain L residue 39 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 65 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 296 optimal weight: 10.0000 chunk 337 optimal weight: 1.9990 chunk 382 optimal weight: 3.9990 chunk 350 optimal weight: 0.0020 chunk 126 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 ASN ** B 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN F 104 ASN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN H 139 ASN K 89 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.174040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.126805 restraints weight = 48633.515| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.77 r_work: 0.3620 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 33698 Z= 0.146 Angle : 0.598 15.694 45751 Z= 0.302 Chirality : 0.043 0.209 5140 Planarity : 0.004 0.074 5723 Dihedral : 12.904 146.035 5022 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.91 % Allowed : 16.51 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % 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: 0.41 (0.14), residues: 3936 helix: 0.98 (0.14), residues: 1372 sheet: -0.33 (0.20), residues: 665 loop : 0.11 (0.15), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 38 TYR 0.013 0.001 TYR B 137 PHE 0.025 0.001 PHE A 219 TRP 0.009 0.001 TRP A 556 HIS 0.005 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (33661) covalent geometry : angle 0.57849 / 0.30 (45703) hydrogen bonds : bond 0.03672 / 2.48 ( 1436) hydrogen bonds : angle 4.71254 / 3.39 ( 4006) metal coordination : bond 0.00670 / 0.38 ( 32) metal coordination : angle 4.81262 / 3.22 ( 45) Misc. bond : bond 0.00054 / 0.03 ( 4) link_TRANS : bond 0.00041 / 0.02 ( 1) link_TRANS : angle 0.20910 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 436 time to evaluate : 1.223 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 71 GLN cc_start: 0.6560 (mp10) cc_final: 0.5775 (pp30) REVERT: A 74 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6770 (mmt) REVERT: A 123 ARG cc_start: 0.7467 (mtm180) cc_final: 0.7062 (mtm180) REVERT: A 124 GLN cc_start: 0.8467 (mt0) cc_final: 0.8172 (mm-40) REVERT: A 133 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8346 (tppp) REVERT: A 175 ARG cc_start: 0.7453 (ttp-110) cc_final: 0.7218 (ptt90) REVERT: A 247 ARG cc_start: 0.7681 (ptt90) cc_final: 0.7253 (ptt-90) REVERT: A 330 LYS cc_start: 0.8123 (pttp) cc_final: 0.7895 (pttt) REVERT: A 373 THR cc_start: 0.8116 (m) cc_final: 0.7828 (p) REVERT: A 386 ASP cc_start: 0.8367 (m-30) cc_final: 0.7772 (t0) REVERT: A 390 GLN cc_start: 0.7632 (tp-100) cc_final: 0.7084 (tp-100) REVERT: A 456 MET cc_start: 0.8993 (mtp) cc_final: 0.8748 (mtm) REVERT: A 476 SER cc_start: 0.8916 (t) cc_final: 0.8686 (p) REVERT: A 495 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8129 (mp0) REVERT: A 542 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7829 (mp0) REVERT: A 589 GLN cc_start: 0.8881 (tt0) cc_final: 0.8526 (tm-30) REVERT: A 592 ASP cc_start: 0.8388 (m-30) cc_final: 0.8127 (m-30) REVERT: A 624 SER cc_start: 0.8927 (p) cc_final: 0.8434 (m) REVERT: A 644 LYS cc_start: 0.7946 (mmmt) cc_final: 0.7482 (mttm) REVERT: A 678 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7126 (tm-30) REVERT: A 688 LYS cc_start: 0.8056 (mmtp) cc_final: 0.7467 (tmtt) REVERT: A 720 ARG cc_start: 0.6988 (ttp-170) cc_final: 0.6615 (ttp80) REVERT: A 755 PHE cc_start: 0.7815 (t80) cc_final: 0.7571 (t80) REVERT: A 833 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7016 (tm-30) REVERT: A 949 ASP cc_start: 0.8001 (p0) cc_final: 0.7464 (m-30) REVERT: A 951 GLU cc_start: 0.7906 (tp30) cc_final: 0.7172 (tp30) REVERT: A 992 ASP cc_start: 0.7513 (m-30) cc_final: 0.7103 (t0) REVERT: A 1034 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6509 (mt-10) REVERT: A 1104 ILE cc_start: 0.8750 (mt) cc_final: 0.8485 (mm) REVERT: A 1112 LYS cc_start: 0.8919 (mmpt) cc_final: 0.8134 (mttp) REVERT: A 1191 TRP cc_start: 0.6685 (m-90) cc_final: 0.6233 (m-90) REVERT: A 1285 MET cc_start: 0.5485 (OUTLIER) cc_final: 0.5228 (ttm) REVERT: A 1290 LYS cc_start: 0.7267 (mmmt) cc_final: 0.6784 (mttt) REVERT: A 1297 GLU cc_start: 0.7553 (mp0) cc_final: 0.7303 (mp0) REVERT: A 1312 ASN cc_start: 0.8247 (t0) cc_final: 0.7580 (t0) REVERT: A 1454 MET cc_start: 0.6725 (pmm) cc_final: 0.5533 (pmm) REVERT: B 89 GLU cc_start: 0.7684 (pt0) cc_final: 0.6835 (pp20) REVERT: B 96 TYR cc_start: 0.7478 (m-80) cc_final: 0.7050 (m-10) REVERT: B 103 ASN cc_start: 0.6802 (m-40) cc_final: 0.6274 (p0) REVERT: B 131 ASP cc_start: 0.8891 (m-30) cc_final: 0.8237 (m-30) REVERT: B 135 ARG cc_start: 0.6828 (mmm160) cc_final: 0.6484 (mtm180) REVERT: B 177 LYS cc_start: 0.8762 (ttmm) cc_final: 0.8492 (mptt) REVERT: B 270 LYS cc_start: 0.7663 (mttt) cc_final: 0.7359 (mttm) REVERT: B 315 LYS cc_start: 0.4535 (mmtt) cc_final: 0.4017 (ptmm) REVERT: B 353 LYS cc_start: 0.8295 (mtpp) cc_final: 0.7878 (mtpp) REVERT: B 398 ARG cc_start: 0.8218 (ttm-80) cc_final: 0.7854 (tpp80) REVERT: B 458 LYS cc_start: 0.7979 (mtpt) cc_final: 0.7322 (mttp) REVERT: B 468 GLU cc_start: 0.5646 (OUTLIER) cc_final: 0.5128 (tt0) REVERT: B 564 GLU cc_start: 0.7932 (tt0) cc_final: 0.7568 (tt0) REVERT: B 615 MET cc_start: 0.7824 (mtt) cc_final: 0.7591 (mtt) REVERT: B 622 LYS cc_start: 0.7345 (mtmm) cc_final: 0.6935 (mmpt) REVERT: B 809 MET cc_start: 0.8295 (ptp) cc_final: 0.7985 (ptp) REVERT: B 860 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7604 (tmm) REVERT: B 864 LYS cc_start: 0.7658 (ptpp) cc_final: 0.6450 (mttt) REVERT: B 904 ARG cc_start: 0.7934 (mtt90) cc_final: 0.7577 (mmt-90) REVERT: B 941 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7360 (tp) REVERT: B 1183 LYS cc_start: 0.7944 (mtpt) cc_final: 0.7515 (ttpp) REVERT: C 50 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7273 (mm-30) REVERT: C 57 VAL cc_start: 0.8381 (m) cc_final: 0.7982 (p) REVERT: C 78 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7249 (tp30) REVERT: C 94 LYS cc_start: 0.7104 (mtpt) cc_final: 0.6504 (ptpp) REVERT: C 177 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6422 (mp0) REVERT: C 205 LYS cc_start: 0.8330 (pttp) cc_final: 0.7858 (mptt) REVERT: D 29 LEU cc_start: 0.5071 (mm) cc_final: 0.4821 (tp) REVERT: D 145 MET cc_start: 0.4158 (tpt) cc_final: 0.3424 (mtt) REVERT: E 39 LEU cc_start: 0.6845 (tm) cc_final: 0.6636 (tm) REVERT: E 45 LYS cc_start: 0.7980 (mmpt) cc_final: 0.7422 (ptpt) REVERT: E 57 MET cc_start: 0.7890 (tmm) cc_final: 0.7324 (tpp) REVERT: E 154 ILE cc_start: 0.8458 (mm) cc_final: 0.8172 (pt) REVERT: E 172 GLU cc_start: 0.8279 (tp30) cc_final: 0.7958 (mm-30) REVERT: E 192 ARG cc_start: 0.8085 (ptm-80) cc_final: 0.7722 (ttm110) REVERT: G 41 LYS cc_start: 0.4383 (tptp) cc_final: 0.3672 (ttpt) REVERT: G 73 LYS cc_start: 0.5875 (mtmt) cc_final: 0.5372 (mtmt) REVERT: H 27 GLU cc_start: 0.8139 (mp0) cc_final: 0.7842 (mp0) REVERT: H 31 THR cc_start: 0.7944 (t) cc_final: 0.7500 (p) REVERT: H 33 GLN cc_start: 0.7490 (mp10) cc_final: 0.6849 (mp10) REVERT: H 52 GLN cc_start: 0.7980 (mm-40) cc_final: 0.7584 (mm-40) REVERT: H 87 ARG cc_start: 0.8287 (mtp85) cc_final: 0.8070 (mtp85) REVERT: H 138 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6848 (pm20) REVERT: I 68 LEU cc_start: 0.7048 (mp) cc_final: 0.6807 (pp) REVERT: I 75 CYS cc_start: 0.5213 (OUTLIER) cc_final: 0.4777 (p) REVERT: I 101 PHE cc_start: 0.6944 (m-10) cc_final: 0.6678 (m-10) REVERT: I 110 PHE cc_start: 0.7445 (p90) cc_final: 0.7188 (p90) REVERT: J 23 ASN cc_start: 0.7765 (t0) cc_final: 0.7158 (m110) REVERT: J 42 LYS cc_start: 0.8235 (ptmt) cc_final: 0.7610 (ptpt) REVERT: K 35 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8298 (m-80) REVERT: K 37 LYS cc_start: 0.7658 (mmtm) cc_final: 0.7361 (mmtt) REVERT: K 55 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7636 (mtpt) REVERT: K 72 LYS cc_start: 0.8870 (mmmm) cc_final: 0.8588 (mttt) REVERT: L 33 GLU cc_start: 0.8043 (tp30) cc_final: 0.7799 (tt0) REVERT: L 62 LYS cc_start: 0.8304 (mmmm) cc_final: 0.8088 (mmtm) outliers start: 102 outliers final: 55 residues processed: 499 average time/residue: 0.6391 time to fit residues: 381.0257 Evaluate side-chains 477 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 410 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 860 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1168 LEU Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain B residue 1221 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 75 CYS Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 35 PHE Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 51 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 123 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 327 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 294 optimal weight: 6.9990 chunk 307 optimal weight: 0.0670 chunk 59 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 192 optimal weight: 0.7980 chunk 237 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 ASN ** B 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN F 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.175435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.128837 restraints weight = 48530.555| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.74 r_work: 0.3653 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 33698 Z= 0.123 Angle : 0.594 14.686 45751 Z= 0.299 Chirality : 0.043 0.211 5140 Planarity : 0.004 0.074 5723 Dihedral : 12.830 146.230 5022 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.48 % Allowed : 17.25 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.14), residues: 3936 helix: 1.07 (0.14), residues: 1379 sheet: -0.28 (0.20), residues: 665 loop : 0.12 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 164 TYR 0.031 0.001 TYR I 15 PHE 0.025 0.001 PHE A 219 TRP 0.008 0.001 TRP A 556 HIS 0.019 0.001 HIS B 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (33661) covalent geometry : angle 0.57715 / 0.30 (45703) hydrogen bonds : bond 0.03480 / 2.37 ( 1436) hydrogen bonds : angle 4.60273 / 3.31 ( 4006) metal coordination : bond 0.00550 / 0.32 ( 32) metal coordination : angle 4.51496 / 3.05 ( 45) Misc. bond : bond 0.00064 / 0.03 ( 4) link_TRANS : bond 0.00034 / 0.02 ( 1) link_TRANS : angle 0.19253 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 456 time to evaluate : 1.126 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: A 41 MET cc_start: 0.6177 (mmm) cc_final: 0.5832 (mtp) REVERT: A 71 GLN cc_start: 0.6482 (mp10) cc_final: 0.6189 (pt0) REVERT: A 72 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6655 (mm-30) REVERT: A 74 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6697 (mmt) REVERT: A 123 ARG cc_start: 0.7471 (mtm180) cc_final: 0.6664 (mtm110) REVERT: A 124 GLN cc_start: 0.8501 (mt0) cc_final: 0.8191 (mm-40) REVERT: A 133 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8310 (tppp) REVERT: A 175 ARG cc_start: 0.7451 (ttp-110) cc_final: 0.7218 (ptt90) REVERT: A 247 ARG cc_start: 0.7627 (ptt90) cc_final: 0.7205 (ptt-90) REVERT: A 277 GLU cc_start: 0.7724 (tt0) cc_final: 0.6886 (pt0) REVERT: A 330 LYS cc_start: 0.8095 (pttp) cc_final: 0.7858 (pttt) REVERT: A 373 THR cc_start: 0.7964 (m) cc_final: 0.7644 (p) REVERT: A 386 ASP cc_start: 0.8355 (m-30) cc_final: 0.7766 (t0) REVERT: A 390 GLN cc_start: 0.7681 (tp-100) cc_final: 0.7164 (tp-100) REVERT: A 415 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7756 (mm) REVERT: A 456 MET cc_start: 0.8958 (mtp) cc_final: 0.8693 (mtm) REVERT: A 542 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7771 (mp0) REVERT: A 589 GLN cc_start: 0.8842 (tt0) cc_final: 0.8498 (tm-30) REVERT: A 592 ASP cc_start: 0.8354 (m-30) cc_final: 0.8093 (m-30) REVERT: A 624 SER cc_start: 0.8842 (p) cc_final: 0.8322 (m) REVERT: A 644 LYS cc_start: 0.7883 (mmmt) cc_final: 0.7453 (mttm) REVERT: A 678 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: A 688 LYS cc_start: 0.8042 (mmtp) cc_final: 0.7464 (tmtt) REVERT: A 720 ARG cc_start: 0.6982 (ttp-170) cc_final: 0.6601 (ttp80) REVERT: A 755 PHE cc_start: 0.7849 (t80) cc_final: 0.7530 (t80) REVERT: A 833 GLU cc_start: 0.7456 (mm-30) cc_final: 0.6996 (tm-30) REVERT: A 951 GLU cc_start: 0.7905 (tp30) cc_final: 0.7318 (tp30) REVERT: A 992 ASP cc_start: 0.7527 (m-30) cc_final: 0.7116 (t0) REVERT: A 1034 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6489 (mt-10) REVERT: A 1104 ILE cc_start: 0.8754 (mt) cc_final: 0.8499 (mm) REVERT: A 1112 LYS cc_start: 0.8835 (mmpt) cc_final: 0.8048 (mttp) REVERT: A 1121 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8316 (tm-30) REVERT: A 1191 TRP cc_start: 0.6697 (m-90) cc_final: 0.6270 (m-90) REVERT: A 1290 LYS cc_start: 0.7300 (mmmt) cc_final: 0.6879 (mttt) REVERT: A 1297 GLU cc_start: 0.7486 (mp0) cc_final: 0.7268 (mp0) REVERT: A 1312 ASN cc_start: 0.8237 (t0) cc_final: 0.7586 (t0) REVERT: A 1454 MET cc_start: 0.6821 (pmm) cc_final: 0.5624 (pmm) REVERT: B 89 GLU cc_start: 0.7737 (pt0) cc_final: 0.6817 (pp20) REVERT: B 96 TYR cc_start: 0.7549 (m-80) cc_final: 0.7057 (m-10) REVERT: B 103 ASN cc_start: 0.6778 (m-40) cc_final: 0.6282 (p0) REVERT: B 131 ASP cc_start: 0.8876 (m-30) cc_final: 0.8189 (m-30) REVERT: B 177 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8486 (mmtm) REVERT: B 270 LYS cc_start: 0.7659 (mttt) cc_final: 0.7357 (mttm) REVERT: B 315 LYS cc_start: 0.4597 (mmtt) cc_final: 0.4016 (ptmm) REVERT: B 319 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5993 (mp0) REVERT: B 327 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7137 (tpt-90) REVERT: B 353 LYS cc_start: 0.8279 (mtpp) cc_final: 0.7842 (mtpp) REVERT: B 458 LYS cc_start: 0.7929 (mtpt) cc_final: 0.7270 (mttp) REVERT: B 468 GLU cc_start: 0.5614 (OUTLIER) cc_final: 0.4957 (tt0) REVERT: B 564 GLU cc_start: 0.7911 (tt0) cc_final: 0.7519 (tt0) REVERT: B 615 MET cc_start: 0.7826 (mtt) cc_final: 0.7609 (mtt) REVERT: B 622 LYS cc_start: 0.7260 (mtmm) cc_final: 0.6860 (mmpt) REVERT: B 691 GLU cc_start: 0.7473 (tt0) cc_final: 0.6996 (tt0) REVERT: B 809 MET cc_start: 0.8200 (ptp) cc_final: 0.7877 (ptp) REVERT: B 864 LYS cc_start: 0.7599 (ptpp) cc_final: 0.6398 (mttt) REVERT: B 941 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7367 (tp) REVERT: B 1009 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7641 (m-30) REVERT: B 1183 LYS cc_start: 0.7917 (mtpt) cc_final: 0.7432 (ttpp) REVERT: B 1190 ASP cc_start: 0.7112 (t0) cc_final: 0.6786 (t0) REVERT: C 50 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7274 (mm-30) REVERT: C 74 SER cc_start: 0.7884 (m) cc_final: 0.7552 (t) REVERT: C 78 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7289 (tp30) REVERT: C 94 LYS cc_start: 0.7102 (mtpt) cc_final: 0.6500 (ptpp) REVERT: C 166 GLU cc_start: 0.7741 (tp30) cc_final: 0.7499 (mm-30) REVERT: C 205 LYS cc_start: 0.8321 (pttp) cc_final: 0.7857 (mptt) REVERT: D 61 GLU cc_start: 0.6998 (pp20) cc_final: 0.6758 (pt0) REVERT: D 145 MET cc_start: 0.4139 (tpt) cc_final: 0.3398 (mtm) REVERT: E 39 LEU cc_start: 0.6853 (tm) cc_final: 0.6625 (tm) REVERT: E 45 LYS cc_start: 0.7976 (mmpt) cc_final: 0.7513 (ptpt) REVERT: E 57 MET cc_start: 0.7782 (tmm) cc_final: 0.7284 (tpp) REVERT: E 104 ASN cc_start: 0.8268 (p0) cc_final: 0.7992 (t0) REVERT: E 154 ILE cc_start: 0.8409 (mm) cc_final: 0.8207 (pt) REVERT: E 172 GLU cc_start: 0.8249 (tp30) cc_final: 0.7954 (mm-30) REVERT: E 192 ARG cc_start: 0.8057 (ptm-80) cc_final: 0.7696 (ttm110) REVERT: G 41 LYS cc_start: 0.4422 (tptp) cc_final: 0.3706 (ttpt) REVERT: G 73 LYS cc_start: 0.5768 (mtmt) cc_final: 0.5192 (mtmt) REVERT: H 27 GLU cc_start: 0.8087 (mp0) cc_final: 0.7757 (mp0) REVERT: H 31 THR cc_start: 0.7956 (t) cc_final: 0.7569 (p) REVERT: H 33 GLN cc_start: 0.7443 (mp10) cc_final: 0.6790 (mp10) REVERT: H 52 GLN cc_start: 0.7967 (mm-40) cc_final: 0.7615 (mm-40) REVERT: H 87 ARG cc_start: 0.8251 (mtp85) cc_final: 0.8015 (mtp85) REVERT: H 138 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6827 (pm20) REVERT: I 68 LEU cc_start: 0.7158 (mp) cc_final: 0.6885 (pp) REVERT: I 75 CYS cc_start: 0.5129 (OUTLIER) cc_final: 0.4701 (p) REVERT: I 110 PHE cc_start: 0.7418 (p90) cc_final: 0.7052 (p90) REVERT: J 23 ASN cc_start: 0.7708 (t0) cc_final: 0.7098 (m110) REVERT: J 31 ASP cc_start: 0.7847 (p0) cc_final: 0.7499 (p0) REVERT: J 42 LYS cc_start: 0.8255 (ptmt) cc_final: 0.7643 (ptpt) REVERT: K 11 LEU cc_start: 0.7983 (mp) cc_final: 0.7604 (mp) REVERT: K 35 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8248 (m-80) REVERT: K 37 LYS cc_start: 0.7829 (mmtm) cc_final: 0.7494 (mmtt) REVERT: K 55 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7485 (mtpt) REVERT: K 108 GLU cc_start: 0.7216 (tp30) cc_final: 0.6980 (tp30) REVERT: L 33 GLU cc_start: 0.8076 (tp30) cc_final: 0.7842 (tt0) REVERT: L 49 LYS cc_start: 0.8096 (mmmm) cc_final: 0.7813 (ptpt) outliers start: 87 outliers final: 40 residues processed: 511 average time/residue: 0.6026 time to fit residues: 368.2740 Evaluate side-chains 471 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 416 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 75 CYS Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 35 PHE Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 51 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 77 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 256 optimal weight: 2.9990 chunk 262 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 396 optimal weight: 20.0000 chunk 231 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 384 optimal weight: 0.9980 chunk 145 optimal weight: 0.4980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 GLN ** B 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1195 HIS ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN E 63 ASN F 104 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.170852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.123791 restraints weight = 48890.938| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.74 r_work: 0.3579 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 33698 Z= 0.231 Angle : 0.664 14.894 45751 Z= 0.333 Chirality : 0.046 0.200 5140 Planarity : 0.005 0.074 5723 Dihedral : 12.922 146.622 5022 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.79 % Allowed : 17.62 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % 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: 0.29 (0.14), residues: 3936 helix: 0.90 (0.14), residues: 1372 sheet: -0.44 (0.20), residues: 661 loop : 0.05 (0.15), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1386 TYR 0.018 0.002 TYR B 137 PHE 0.026 0.002 PHE A 219 TRP 0.008 0.001 TRP B 31 HIS 0.013 0.001 HIS B 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 (33661) covalent geometry : angle 0.64529 / 0.33 (45703) hydrogen bonds : bond 0.04029 / 2.71 ( 1436) hydrogen bonds : angle 4.81875 / 3.46 ( 4006) metal coordination : bond 0.00845 / 0.47 ( 32) metal coordination : angle 5.04544 / 3.36 ( 45) Misc. bond : bond 0.00054 / 0.03 ( 4) link_TRANS : bond 0.00102 / 0.05 ( 1) link_TRANS : angle 0.14568 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 424 time to evaluate : 0.816 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 41 MET cc_start: 0.6283 (mmm) cc_final: 0.5862 (mtp) REVERT: A 74 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6617 (mmt) REVERT: A 123 ARG cc_start: 0.7520 (mtm180) cc_final: 0.6624 (mtt90) REVERT: A 124 GLN cc_start: 0.8535 (mt0) cc_final: 0.8203 (mm-40) REVERT: A 133 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8344 (tppp) REVERT: A 175 ARG cc_start: 0.7533 (ttp-110) cc_final: 0.7259 (ptt90) REVERT: A 247 ARG cc_start: 0.7745 (ptt90) cc_final: 0.7538 (ptt-90) REVERT: A 290 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7960 (tm-30) REVERT: A 373 THR cc_start: 0.8012 (m) cc_final: 0.7691 (p) REVERT: A 386 ASP cc_start: 0.8423 (m-30) cc_final: 0.7805 (t0) REVERT: A 390 GLN cc_start: 0.7647 (tp-100) cc_final: 0.7070 (tp-100) REVERT: A 415 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8029 (mm) REVERT: A 456 MET cc_start: 0.9025 (mtp) cc_final: 0.8749 (mtm) REVERT: A 495 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: A 542 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7896 (mp0) REVERT: A 589 GLN cc_start: 0.8935 (tt0) cc_final: 0.8570 (tm-30) REVERT: A 592 ASP cc_start: 0.8387 (m-30) cc_final: 0.8078 (m-30) REVERT: A 624 SER cc_start: 0.8957 (p) cc_final: 0.8535 (m) REVERT: A 644 LYS cc_start: 0.8083 (mmmt) cc_final: 0.7588 (mttm) REVERT: A 678 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: A 688 LYS cc_start: 0.8019 (mmtp) cc_final: 0.7467 (tmtt) REVERT: A 755 PHE cc_start: 0.7917 (t80) cc_final: 0.7659 (t80) REVERT: A 833 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7002 (tm-30) REVERT: A 949 ASP cc_start: 0.8174 (p0) cc_final: 0.7680 (m-30) REVERT: A 951 GLU cc_start: 0.7860 (tp30) cc_final: 0.7103 (tp30) REVERT: A 992 ASP cc_start: 0.7563 (m-30) cc_final: 0.7176 (t0) REVERT: A 1034 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6463 (mt-10) REVERT: A 1104 ILE cc_start: 0.8751 (mt) cc_final: 0.8485 (mm) REVERT: A 1112 LYS cc_start: 0.8796 (mmpt) cc_final: 0.8090 (mttp) REVERT: A 1121 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8255 (tm-30) REVERT: A 1191 TRP cc_start: 0.6747 (m-90) cc_final: 0.6332 (m-90) REVERT: A 1290 LYS cc_start: 0.7299 (mmmt) cc_final: 0.6704 (mttp) REVERT: A 1312 ASN cc_start: 0.8277 (t0) cc_final: 0.7858 (t0) REVERT: A 1404 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7369 (mt-10) REVERT: A 1408 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8278 (mp) REVERT: A 1454 MET cc_start: 0.6943 (pmm) cc_final: 0.5776 (pmm) REVERT: B 96 TYR cc_start: 0.7588 (m-80) cc_final: 0.7137 (m-10) REVERT: B 103 ASN cc_start: 0.6859 (m-40) cc_final: 0.6394 (p0) REVERT: B 131 ASP cc_start: 0.8870 (m-30) cc_final: 0.8189 (m-30) REVERT: B 137 TYR cc_start: 0.7154 (m-80) cc_final: 0.6930 (m-80) REVERT: B 177 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8442 (mptt) REVERT: B 222 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7561 (pt) REVERT: B 270 LYS cc_start: 0.7743 (mttt) cc_final: 0.7413 (mttm) REVERT: B 289 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8016 (mm) REVERT: B 315 LYS cc_start: 0.4591 (mmtt) cc_final: 0.4151 (ptmm) REVERT: B 353 LYS cc_start: 0.8303 (mtpp) cc_final: 0.7857 (mtpp) REVERT: B 458 LYS cc_start: 0.7977 (mtpt) cc_final: 0.7328 (mttp) REVERT: B 468 GLU cc_start: 0.5790 (OUTLIER) cc_final: 0.4070 (pt0) REVERT: B 564 GLU cc_start: 0.7936 (tt0) cc_final: 0.7573 (tt0) REVERT: B 615 MET cc_start: 0.7800 (mtt) cc_final: 0.7581 (mtt) REVERT: B 622 LYS cc_start: 0.7329 (mtmm) cc_final: 0.6914 (mmpt) REVERT: B 699 GLU cc_start: 0.7978 (pt0) cc_final: 0.7735 (pp20) REVERT: B 809 MET cc_start: 0.8389 (ptp) cc_final: 0.8082 (ptp) REVERT: B 864 LYS cc_start: 0.7712 (ptpp) cc_final: 0.6471 (mttt) REVERT: B 941 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7405 (tp) REVERT: B 1190 ASP cc_start: 0.7245 (t0) cc_final: 0.6739 (t0) REVERT: C 50 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7316 (mm-30) REVERT: C 78 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7306 (tp30) REVERT: C 94 LYS cc_start: 0.7155 (mtpt) cc_final: 0.6527 (ptpp) REVERT: C 135 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8056 (mm-40) REVERT: C 148 ARG cc_start: 0.6127 (ttt90) cc_final: 0.5858 (ttt90) REVERT: C 166 GLU cc_start: 0.7889 (tp30) cc_final: 0.7586 (mm-30) REVERT: C 177 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6496 (mp0) REVERT: D 145 MET cc_start: 0.4244 (tpt) cc_final: 0.3618 (mtm) REVERT: D 218 GLU cc_start: 0.3605 (tp30) cc_final: 0.2865 (mm-30) REVERT: E 57 MET cc_start: 0.7964 (tmm) cc_final: 0.7699 (tpp) REVERT: E 58 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6905 (pmm) REVERT: E 104 ASN cc_start: 0.8284 (p0) cc_final: 0.7943 (t0) REVERT: E 154 ILE cc_start: 0.8466 (mm) cc_final: 0.8139 (pt) REVERT: E 172 GLU cc_start: 0.8368 (tp30) cc_final: 0.8054 (mm-30) REVERT: E 192 ARG cc_start: 0.8081 (ptm-80) cc_final: 0.7699 (ttm110) REVERT: G 41 LYS cc_start: 0.4238 (tptp) cc_final: 0.3540 (ttpt) REVERT: G 73 LYS cc_start: 0.5972 (mtmt) cc_final: 0.5506 (mtmt) REVERT: H 27 GLU cc_start: 0.8150 (mp0) cc_final: 0.7820 (mp0) REVERT: H 33 GLN cc_start: 0.7549 (mp10) cc_final: 0.6893 (mp10) REVERT: H 52 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7699 (mm-40) REVERT: H 87 ARG cc_start: 0.8321 (mtp85) cc_final: 0.8116 (mtp85) REVERT: H 138 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6963 (pm20) REVERT: I 75 CYS cc_start: 0.5438 (OUTLIER) cc_final: 0.5078 (p) REVERT: I 110 PHE cc_start: 0.7407 (p90) cc_final: 0.7184 (p90) REVERT: J 23 ASN cc_start: 0.7785 (t0) cc_final: 0.7152 (m110) REVERT: J 31 ASP cc_start: 0.7929 (p0) cc_final: 0.7530 (p0) REVERT: J 42 LYS cc_start: 0.8310 (ptmt) cc_final: 0.7722 (ptpt) REVERT: K 35 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: K 55 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7581 (mtpt) REVERT: L 33 GLU cc_start: 0.7986 (tp30) cc_final: 0.7704 (tt0) REVERT: L 49 LYS cc_start: 0.8180 (mmmm) cc_final: 0.7874 (ptpt) outliers start: 98 outliers final: 51 residues processed: 486 average time/residue: 0.5979 time to fit residues: 349.2730 Evaluate side-chains 472 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 403 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1408 ILE Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 75 CYS Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 35 PHE Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 51 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 267 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 305 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 316 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 309 optimal weight: 0.7980 chunk 211 optimal weight: 0.7980 chunk 229 optimal weight: 20.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN F 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.172444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.125665 restraints weight = 48242.306| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.74 r_work: 0.3609 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 33698 Z= 0.162 Angle : 0.647 14.485 45751 Z= 0.324 Chirality : 0.044 0.208 5140 Planarity : 0.004 0.095 5723 Dihedral : 12.888 147.709 5022 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.25 % Allowed : 18.59 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.14), residues: 3936 helix: 0.95 (0.14), residues: 1373 sheet: -0.41 (0.20), residues: 649 loop : 0.03 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 19 TYR 0.033 0.001 TYR I 15 PHE 0.026 0.002 PHE A 219 TRP 0.012 0.001 TRP E 13 HIS 0.013 0.001 HIS B 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (33661) covalent geometry : angle 0.63012 / 0.32 (45703) hydrogen bonds : bond 0.03728 / 2.52 ( 1436) hydrogen bonds : angle 4.72729 / 3.39 ( 4006) metal coordination : bond 0.00649 / 0.36 ( 32) metal coordination : angle 4.79471 / 3.23 ( 45) Misc. bond : bond 0.00057 / 0.03 ( 4) link_TRANS : bond 0.00075 / 0.04 ( 1) link_TRANS : angle 0.17820 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 415 time to evaluate : 0.903 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: A 74 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6689 (mmt) REVERT: A 123 ARG cc_start: 0.7482 (mtm180) cc_final: 0.7181 (mtm180) REVERT: A 124 GLN cc_start: 0.8525 (mt0) cc_final: 0.8181 (mm-40) REVERT: A 133 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8307 (tppp) REVERT: A 175 ARG cc_start: 0.7492 (ttp-110) cc_final: 0.7223 (ptt90) REVERT: A 290 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7935 (tm-30) REVERT: A 330 LYS cc_start: 0.8285 (pttp) cc_final: 0.8026 (pttt) REVERT: A 373 THR cc_start: 0.7966 (m) cc_final: 0.7668 (p) REVERT: A 386 ASP cc_start: 0.8407 (m-30) cc_final: 0.7791 (t0) REVERT: A 390 GLN cc_start: 0.7411 (tp-100) cc_final: 0.6885 (tp-100) REVERT: A 415 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7948 (mm) REVERT: A 456 MET cc_start: 0.9005 (mtp) cc_final: 0.8721 (mtm) REVERT: A 542 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7806 (mp0) REVERT: A 589 GLN cc_start: 0.8929 (tt0) cc_final: 0.8561 (tm-30) REVERT: A 592 ASP cc_start: 0.8369 (m-30) cc_final: 0.8080 (m-30) REVERT: A 624 SER cc_start: 0.8923 (p) cc_final: 0.8496 (m) REVERT: A 644 LYS cc_start: 0.7952 (mmmt) cc_final: 0.7481 (mttm) REVERT: A 678 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: A 688 LYS cc_start: 0.7990 (mmtp) cc_final: 0.7476 (tmtt) REVERT: A 755 PHE cc_start: 0.7837 (t80) cc_final: 0.7549 (t80) REVERT: A 833 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7022 (tp30) REVERT: A 949 ASP cc_start: 0.8151 (p0) cc_final: 0.7600 (m-30) REVERT: A 951 GLU cc_start: 0.7834 (tp30) cc_final: 0.7091 (tp30) REVERT: A 992 ASP cc_start: 0.7542 (m-30) cc_final: 0.7147 (t0) REVERT: A 1034 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6485 (mt-10) REVERT: A 1104 ILE cc_start: 0.8744 (mt) cc_final: 0.8476 (mm) REVERT: A 1121 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8211 (mt-10) REVERT: A 1191 TRP cc_start: 0.6730 (m-90) cc_final: 0.6245 (m-90) REVERT: A 1290 LYS cc_start: 0.7228 (mmmt) cc_final: 0.6645 (mttp) REVERT: A 1312 ASN cc_start: 0.8314 (t0) cc_final: 0.7850 (t0) REVERT: A 1454 MET cc_start: 0.6871 (pmm) cc_final: 0.5673 (pmm) REVERT: B 69 LEU cc_start: 0.8455 (mt) cc_final: 0.8123 (mp) REVERT: B 96 TYR cc_start: 0.7587 (m-80) cc_final: 0.7218 (m-10) REVERT: B 103 ASN cc_start: 0.6852 (m-40) cc_final: 0.6348 (p0) REVERT: B 177 LYS cc_start: 0.8754 (ttmm) cc_final: 0.8435 (mptt) REVERT: B 270 LYS cc_start: 0.7729 (mttt) cc_final: 0.7410 (mttm) REVERT: B 315 LYS cc_start: 0.4562 (mmtt) cc_final: 0.4148 (ptmm) REVERT: B 353 LYS cc_start: 0.8285 (mtpp) cc_final: 0.7891 (mtpp) REVERT: B 458 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7303 (mttp) REVERT: B 468 GLU cc_start: 0.5754 (OUTLIER) cc_final: 0.4064 (pt0) REVERT: B 564 GLU cc_start: 0.7972 (tt0) cc_final: 0.7669 (tt0) REVERT: B 615 MET cc_start: 0.7831 (mtt) cc_final: 0.7611 (mtt) REVERT: B 621 GLU cc_start: 0.7979 (pt0) cc_final: 0.7536 (pm20) REVERT: B 622 LYS cc_start: 0.7325 (mtmm) cc_final: 0.6890 (mmpt) REVERT: B 699 GLU cc_start: 0.7942 (pt0) cc_final: 0.7660 (pp20) REVERT: B 809 MET cc_start: 0.8311 (ptp) cc_final: 0.7999 (ptp) REVERT: B 864 LYS cc_start: 0.7684 (ptpp) cc_final: 0.6473 (mttt) REVERT: B 941 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7442 (tp) REVERT: B 1190 ASP cc_start: 0.7238 (t0) cc_final: 0.6737 (t0) REVERT: C 50 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7327 (mm-30) REVERT: C 78 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7323 (tp30) REVERT: C 94 LYS cc_start: 0.7159 (mtpt) cc_final: 0.6531 (ptpp) REVERT: C 148 ARG cc_start: 0.6123 (ttt90) cc_final: 0.5868 (ttt90) REVERT: C 166 GLU cc_start: 0.7909 (tp30) cc_final: 0.7585 (mm-30) REVERT: C 177 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6444 (mp0) REVERT: D 29 LEU cc_start: 0.4677 (tp) cc_final: 0.4305 (mp) REVERT: D 61 GLU cc_start: 0.7048 (pp20) cc_final: 0.6786 (pt0) REVERT: D 145 MET cc_start: 0.4271 (tpt) cc_final: 0.3619 (mtm) REVERT: D 218 GLU cc_start: 0.3616 (tp30) cc_final: 0.2936 (mm-30) REVERT: E 39 LEU cc_start: 0.6753 (tm) cc_final: 0.6533 (tm) REVERT: E 45 LYS cc_start: 0.8025 (mmpt) cc_final: 0.7445 (ptpt) REVERT: E 58 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6734 (pmm) REVERT: E 104 ASN cc_start: 0.8253 (p0) cc_final: 0.7932 (t0) REVERT: E 154 ILE cc_start: 0.8427 (mm) cc_final: 0.8144 (pt) REVERT: E 172 GLU cc_start: 0.8298 (tp30) cc_final: 0.8086 (mm-30) REVERT: E 192 ARG cc_start: 0.8049 (ptm-80) cc_final: 0.7675 (ttm110) REVERT: G 41 LYS cc_start: 0.4318 (tptp) cc_final: 0.3619 (ttpt) REVERT: G 73 LYS cc_start: 0.5952 (mtmt) cc_final: 0.5424 (mtmt) REVERT: H 27 GLU cc_start: 0.8155 (mp0) cc_final: 0.7805 (mp0) REVERT: H 33 GLN cc_start: 0.7473 (mp10) cc_final: 0.6803 (mp10) REVERT: H 52 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7604 (mm-40) REVERT: H 87 ARG cc_start: 0.8320 (mtp85) cc_final: 0.8114 (mtp85) REVERT: H 138 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6914 (pm20) REVERT: I 75 CYS cc_start: 0.5486 (OUTLIER) cc_final: 0.5275 (p) REVERT: I 101 PHE cc_start: 0.7086 (m-10) cc_final: 0.6834 (m-10) REVERT: I 110 PHE cc_start: 0.7377 (p90) cc_final: 0.7158 (p90) REVERT: J 23 ASN cc_start: 0.7768 (t0) cc_final: 0.7129 (m110) REVERT: J 31 ASP cc_start: 0.7914 (p0) cc_final: 0.7534 (p0) REVERT: J 42 LYS cc_start: 0.8320 (ptmt) cc_final: 0.7712 (ptpt) REVERT: K 11 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7577 (mp) REVERT: K 35 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8282 (m-80) REVERT: K 37 LYS cc_start: 0.7755 (mmtm) cc_final: 0.7456 (mmtt) REVERT: K 55 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7558 (mtpt) REVERT: L 33 GLU cc_start: 0.8030 (tp30) cc_final: 0.7793 (tt0) REVERT: L 49 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7871 (ptpt) outliers start: 79 outliers final: 47 residues processed: 466 average time/residue: 0.6014 time to fit residues: 335.7115 Evaluate side-chains 457 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 396 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 75 CYS Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 35 PHE Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 51 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 229 optimal weight: 20.0000 chunk 18 optimal weight: 0.7980 chunk 353 optimal weight: 5.9990 chunk 303 optimal weight: 0.8980 chunk 173 optimal weight: 10.0000 chunk 326 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 GLN ** B 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN E 63 ASN F 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.172527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.125404 restraints weight = 49671.322| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.89 r_work: 0.3570 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 33698 Z= 0.141 Angle : 0.644 14.749 45751 Z= 0.323 Chirality : 0.044 0.209 5140 Planarity : 0.004 0.081 5723 Dihedral : 12.842 148.135 5022 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.19 % Allowed : 18.79 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.14), residues: 3936 helix: 1.00 (0.14), residues: 1374 sheet: -0.39 (0.20), residues: 649 loop : 0.03 (0.15), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 19 TYR 0.018 0.001 TYR B 811 PHE 0.025 0.001 PHE A 219 TRP 0.012 0.001 TRP E 13 HIS 0.011 0.001 HIS B 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (33661) covalent geometry : angle 0.62837 / 0.32 (45703) hydrogen bonds : bond 0.03598 / 2.45 ( 1436) hydrogen bonds : angle 4.69545 / 3.37 ( 4006) metal coordination : bond 0.00600 / 0.34 ( 32) metal coordination : angle 4.54053 / 3.08 ( 45) Misc. bond : bond 0.00065 / 0.03 ( 4) link_TRANS : bond 0.00057 / 0.03 ( 1) link_TRANS : angle 0.17826 / 0.09 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 417 time to evaluate : 1.494 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 74 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6687 (mmt) REVERT: A 123 ARG cc_start: 0.7407 (mtm180) cc_final: 0.7168 (mtm180) REVERT: A 124 GLN cc_start: 0.8449 (mt0) cc_final: 0.8117 (mm-40) REVERT: A 133 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8311 (tppp) REVERT: A 175 ARG cc_start: 0.7451 (ttp-110) cc_final: 0.7149 (ptt90) REVERT: A 373 THR cc_start: 0.7912 (m) cc_final: 0.7592 (p) REVERT: A 386 ASP cc_start: 0.8498 (m-30) cc_final: 0.7815 (t0) REVERT: A 390 GLN cc_start: 0.7242 (tp-100) cc_final: 0.6771 (tp-100) REVERT: A 415 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7779 (mm) REVERT: A 456 MET cc_start: 0.8920 (mtp) cc_final: 0.8664 (mtm) REVERT: A 542 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7522 (mp0) REVERT: A 589 GLN cc_start: 0.8966 (tt0) cc_final: 0.8499 (tm-30) REVERT: A 592 ASP cc_start: 0.8359 (m-30) cc_final: 0.8002 (m-30) REVERT: A 624 SER cc_start: 0.8870 (p) cc_final: 0.8354 (m) REVERT: A 644 LYS cc_start: 0.7723 (mmmt) cc_final: 0.7194 (mttp) REVERT: A 678 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: A 688 LYS cc_start: 0.7967 (mmtp) cc_final: 0.7432 (tmtt) REVERT: A 755 PHE cc_start: 0.7665 (t80) cc_final: 0.7294 (t80) REVERT: A 791 ASP cc_start: 0.7705 (t0) cc_final: 0.6981 (m-30) REVERT: A 833 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6893 (tm-30) REVERT: A 949 ASP cc_start: 0.8192 (p0) cc_final: 0.7550 (m-30) REVERT: A 951 GLU cc_start: 0.7746 (tp30) cc_final: 0.6934 (tp30) REVERT: A 992 ASP cc_start: 0.7402 (m-30) cc_final: 0.6967 (t0) REVERT: A 1034 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6251 (mt-10) REVERT: A 1104 ILE cc_start: 0.8585 (mt) cc_final: 0.8315 (mm) REVERT: A 1191 TRP cc_start: 0.6684 (m-90) cc_final: 0.6211 (m-90) REVERT: A 1284 MET cc_start: 0.8150 (tpp) cc_final: 0.7859 (tpp) REVERT: A 1290 LYS cc_start: 0.7085 (mmmt) cc_final: 0.6498 (mttp) REVERT: A 1297 GLU cc_start: 0.7595 (mp0) cc_final: 0.7297 (mp0) REVERT: A 1312 ASN cc_start: 0.8030 (t0) cc_final: 0.7593 (t0) REVERT: A 1454 MET cc_start: 0.6975 (pmm) cc_final: 0.5785 (pmm) REVERT: B 69 LEU cc_start: 0.8205 (mt) cc_final: 0.7972 (mp) REVERT: B 96 TYR cc_start: 0.7496 (m-80) cc_final: 0.7132 (m-10) REVERT: B 103 ASN cc_start: 0.6778 (m-40) cc_final: 0.6232 (p0) REVERT: B 177 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8406 (mptt) REVERT: B 222 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7237 (pt) REVERT: B 270 LYS cc_start: 0.7509 (mttt) cc_final: 0.7179 (mttm) REVERT: B 315 LYS cc_start: 0.4502 (mmtt) cc_final: 0.3987 (ptmm) REVERT: B 319 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.6169 (mp0) REVERT: B 353 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7804 (mtpp) REVERT: B 398 ARG cc_start: 0.8094 (ttm-80) cc_final: 0.7859 (tpp80) REVERT: B 458 LYS cc_start: 0.7728 (mtpt) cc_final: 0.7072 (mttp) REVERT: B 468 GLU cc_start: 0.5561 (OUTLIER) cc_final: 0.3961 (pt0) REVERT: B 621 GLU cc_start: 0.8007 (pt0) cc_final: 0.7482 (pm20) REVERT: B 622 LYS cc_start: 0.7153 (mtmm) cc_final: 0.6717 (mmpt) REVERT: B 699 GLU cc_start: 0.8000 (pt0) cc_final: 0.7672 (pp20) REVERT: B 809 MET cc_start: 0.8235 (ptp) cc_final: 0.7859 (ptp) REVERT: B 864 LYS cc_start: 0.7582 (ptpp) cc_final: 0.6443 (mttt) REVERT: B 865 LYS cc_start: 0.8374 (tttt) cc_final: 0.7868 (tptp) REVERT: B 941 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7423 (tp) REVERT: B 1190 ASP cc_start: 0.7144 (t0) cc_final: 0.6582 (t0) REVERT: C 50 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7073 (mm-30) REVERT: C 78 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7366 (tp30) REVERT: C 94 LYS cc_start: 0.7014 (mtpt) cc_final: 0.6394 (ptpp) REVERT: C 148 ARG cc_start: 0.5849 (ttt90) cc_final: 0.5626 (ttt90) REVERT: C 166 GLU cc_start: 0.7951 (tp30) cc_final: 0.7565 (mm-30) REVERT: C 177 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6212 (mp0) REVERT: C 205 LYS cc_start: 0.8230 (pttp) cc_final: 0.7703 (mptt) REVERT: D 29 LEU cc_start: 0.4515 (tp) cc_final: 0.4208 (mp) REVERT: D 61 GLU cc_start: 0.7079 (pp20) cc_final: 0.6814 (pt0) REVERT: D 145 MET cc_start: 0.4258 (tpt) cc_final: 0.3645 (mtm) REVERT: D 218 GLU cc_start: 0.3618 (tp30) cc_final: 0.2914 (mm-30) REVERT: E 45 LYS cc_start: 0.8035 (mmpt) cc_final: 0.7360 (ptpt) REVERT: E 57 MET cc_start: 0.7758 (tpp) cc_final: 0.7456 (ttp) REVERT: E 102 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: E 104 ASN cc_start: 0.8349 (p0) cc_final: 0.8039 (t0) REVERT: E 154 ILE cc_start: 0.8217 (mm) cc_final: 0.7941 (pt) REVERT: E 172 GLU cc_start: 0.8386 (tp30) cc_final: 0.8032 (mm-30) REVERT: E 192 ARG cc_start: 0.8010 (ptm-80) cc_final: 0.7557 (ttm110) REVERT: E 215 MET cc_start: 0.6713 (mtp) cc_final: 0.6248 (mtm) REVERT: F 114 GLU cc_start: 0.8738 (tt0) cc_final: 0.8528 (tt0) REVERT: G 41 LYS cc_start: 0.4352 (tptp) cc_final: 0.3674 (ttpt) REVERT: G 73 LYS cc_start: 0.5711 (mtmt) cc_final: 0.5234 (mtmt) REVERT: H 27 GLU cc_start: 0.7912 (mp0) cc_final: 0.7523 (mp0) REVERT: H 33 GLN cc_start: 0.7233 (mp10) cc_final: 0.6545 (mp10) REVERT: H 52 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7445 (mm-40) REVERT: H 87 ARG cc_start: 0.8377 (mtp85) cc_final: 0.8155 (mtp85) REVERT: I 101 PHE cc_start: 0.6848 (m-10) cc_final: 0.6579 (m-10) REVERT: I 110 PHE cc_start: 0.7122 (p90) cc_final: 0.6915 (p90) REVERT: J 23 ASN cc_start: 0.7616 (t0) cc_final: 0.6927 (m110) REVERT: J 31 ASP cc_start: 0.7859 (p0) cc_final: 0.7425 (p0) REVERT: J 42 LYS cc_start: 0.8280 (ptmt) cc_final: 0.7632 (ptpt) REVERT: K 11 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7216 (mp) REVERT: K 18 LYS cc_start: 0.7885 (tppt) cc_final: 0.7477 (tppt) REVERT: K 35 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8194 (m-80) REVERT: K 36 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7624 (mp0) REVERT: K 37 LYS cc_start: 0.7542 (mmtm) cc_final: 0.7195 (mmtt) REVERT: K 55 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7203 (mtpt) REVERT: K 72 LYS cc_start: 0.8656 (mtpp) cc_final: 0.8383 (mttt) REVERT: L 33 GLU cc_start: 0.8008 (tp30) cc_final: 0.7762 (tt0) REVERT: L 49 LYS cc_start: 0.8181 (mmmm) cc_final: 0.7766 (ptpt) outliers start: 77 outliers final: 46 residues processed: 470 average time/residue: 0.6951 time to fit residues: 390.8884 Evaluate side-chains 457 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 397 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1259 MET Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 ASN Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 35 PHE Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 51 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 320 optimal weight: 6.9990 chunk 335 optimal weight: 10.0000 chunk 210 optimal weight: 0.0010 chunk 82 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 395 optimal weight: 10.0000 chunk 244 optimal weight: 0.7980 chunk 192 optimal weight: 0.9990 chunk 23 optimal weight: 0.0070 overall best weight: 0.5006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 GLN ** B 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN F 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.173910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.127066 restraints weight = 49135.907| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.88 r_work: 0.3614 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33698 Z= 0.125 Angle : 0.637 16.015 45751 Z= 0.319 Chirality : 0.044 0.212 5140 Planarity : 0.004 0.074 5723 Dihedral : 12.792 148.180 5022 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.74 % Allowed : 19.38 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % 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: 0.41 (0.14), residues: 3936 helix: 1.05 (0.14), residues: 1380 sheet: -0.33 (0.20), residues: 644 loop : 0.04 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 7 TYR 0.034 0.001 TYR I 15 PHE 0.025 0.001 PHE A 219 TRP 0.010 0.001 TRP E 79 HIS 0.010 0.001 HIS B 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (33661) covalent geometry : angle 0.61763 / 0.32 (45703) hydrogen bonds : bond 0.03475 / 2.36 ( 1436) hydrogen bonds : angle 4.63635 / 3.34 ( 4006) metal coordination : bond 0.00602 / 0.37 ( 32) metal coordination : angle 5.05294 / 3.42 ( 45) Misc. bond : bond 0.00076 / 0.04 ( 4) link_TRANS : bond 0.00037 / 0.02 ( 1) link_TRANS : angle 0.18104 / 0.09 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11409.45 seconds wall clock time: 194 minutes 49.56 seconds (11689.56 seconds total)