Starting phenix.real_space_refine on Sun Aug 9 07:52:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24qr_69771/08_2026/24qr_69771.cif Found real_map, /net/cci-nas-00/data/ceres_data/24qr_69771/08_2026/24qr_69771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/24qr_69771/08_2026/24qr_69771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24qr_69771/08_2026/24qr_69771.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/24qr_69771/08_2026/24qr_69771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24qr_69771/08_2026/24qr_69771.map" } resolution = 2.67 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= 0.001 sd= 0.027 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: 8 Type Number sf(0) Gaussians Pt 1 10.81 5 Zn 8 6.06 5 P 51 5.49 5 Mg 1 5.21 5 S 181 5.16 5 C 20547 2.51 5 N 5734 2.21 5 O 6330 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: 32853 Number of models: 1 Model: "" Number of chains: 22 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: "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: "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: "N" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 342 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "P" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 248 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 11} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 470 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 11205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1424, 11205 Classifications: {'peptide': 1424} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1357} Chain breaks: 3 Chain: "B" Number of atoms: 9453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1187, 9453 Classifications: {'peptide': 1187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1134} Chain breaks: 3 Chain: "D" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1326 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Chain: "H" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1113 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' PT': 1, 'DNH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 647 SG CYS C 86 73.163 56.829 131.626 1.00 53.87 S ATOM 664 SG CYS C 88 71.162 59.539 129.817 1.00 49.94 S ATOM 697 SG CYS C 92 72.201 59.836 133.502 1.00 47.50 S ATOM 720 SG CYS C 95 74.749 60.170 130.577 1.00 48.95 S ATOM 5935 SG CYS I 7 114.182 124.963 37.248 1.00 84.85 S ATOM 5960 SG CYS I 10 110.491 124.201 38.034 1.00 98.20 S ATOM 6126 SG CYS I 29 112.254 122.497 35.181 1.00 96.24 S ATOM 6150 SG CYS I 32 111.118 126.273 35.201 1.00100.05 S ATOM 6477 SG CYS I 75 140.294 108.571 69.564 1.00 63.00 S ATOM 6499 SG CYS I 78 141.083 112.378 70.635 1.00 82.95 S ATOM 6715 SG CYS I 103 138.004 110.291 71.971 1.00 69.84 S ATOM 6735 SG CYS I 106 138.440 111.868 68.596 1.00 59.21 S ATOM 6880 SG CYS J 7 100.393 72.531 118.648 1.00 46.09 S ATOM 6903 SG CYS J 10 101.383 69.846 121.208 1.00 38.67 S ATOM 7183 SG CYS J 45 103.931 71.305 118.710 1.00 39.53 S ATOM 7189 SG CYS J 46 102.623 73.216 121.767 1.00 43.08 S ATOM 8369 SG CYS L 31 67.361 100.722 113.407 1.00 78.79 S ATOM 8389 SG CYS L 34 67.345 103.395 116.381 1.00 75.62 S ATOM 8493 SG CYS L 48 64.162 102.346 114.455 1.00 71.24 S ATOM 8516 SG CYS L 51 66.973 104.537 113.088 1.00 81.57 S ATOM 10558 SG CYS A 107 66.963 78.448 26.274 1.00 50.68 S ATOM 10582 SG CYS A 110 64.936 75.529 25.069 1.00 45.74 S ATOM 10887 SG CYS A 148 68.206 76.364 23.260 1.00 52.24 S ATOM 11025 SG CYS A 167 65.244 78.644 22.904 1.00 62.50 S ATOM 10253 SG CYS A 67 48.172 66.064 67.869 1.00 48.72 S ATOM 10275 SG CYS A 70 48.986 62.322 68.204 1.00 44.30 S ATOM 10328 SG CYS A 77 51.793 64.975 68.561 1.00 51.38 S ATOM 29902 SG CYS B1163 54.700 56.189 54.711 1.00 41.23 S ATOM 29920 SG CYS B1166 55.999 59.375 53.369 1.00 45.52 S ATOM 30045 SG CYS B1182 52.417 59.112 55.053 1.00 46.01 S ATOM 30064 SG CYS B1185 53.134 58.006 51.529 1.00 50.24 S Time building chain proxies: 5.95, per 1000 atoms: 0.18 Number of scatterers: 32853 At special positions: 0 Unit cell: (155.31, 151.59, 154.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Pt 1 77.96 Zn 8 29.99 S 181 16.00 P 51 15.00 Mg 1 11.99 O 6330 8.00 N 5734 7.00 C 20547 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.78 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 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " 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 B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " 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 32 " 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 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " 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 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " 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 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7512 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 52 sheets defined 38.8% alpha, 19.0% beta 22 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 114 through 118 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: 3.713A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 268 removed outlier: 3.548A pdb=" N ASP C 268 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 26 Processing helix chain 'E' and resid 31 through 36 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 104 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.592A 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: 3.594A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 31 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 62 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.672A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 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 106 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.569A pdb=" N GLN A 124 " --> pdb=" O GLU A 120 " (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 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: 3.574A 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 524 through 535 removed outlier: 3.622A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.530A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 removed outlier: 4.023A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (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 661 Processing helix chain 'A' and resid 665 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 Processing helix chain 'A' and resid 809 through 846 removed outlier: 5.044A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) 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: 3.946A pdb=" N LEU A 913 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 997 removed outlier: 3.729A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1096 through 1106 removed outlier: 3.603A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1125 removed outlier: 3.996A 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 1143 through 1146 No H-bonds generated for 'chain 'A' and resid 1143 through 1146' Processing helix chain 'A' and resid 1166 through 1176 Processing helix chain 'A' and resid 1184 through 1188 removed outlier: 3.694A pdb=" N GLN A1187 " --> pdb=" O SER A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1250 through 1255 removed outlier: 3.514A pdb=" N ALA A1254 " --> pdb=" O ALA A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1269 removed outlier: 3.720A pdb=" N GLU A1269 " --> pdb=" O ASN A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1318 removed outlier: 3.831A 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: 4.577A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1377 removed outlier: 3.925A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.618A 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: 3.703A pdb=" N MET A1454 " --> pdb=" O LEU A1450 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 41 removed outlier: 3.764A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (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: 3.549A 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: 5.495A 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 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 337 Processing helix chain 'B' and resid 344 through 359 removed outlier: 4.506A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.557A pdb=" N LYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) 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 removed outlier: 4.101A pdb=" N GLU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 449 through 463 removed outlier: 4.322A pdb=" N ILE B 453 " --> pdb=" O ASN B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 503 through 509 removed outlier: 3.793A pdb=" N LEU B 508 " --> pdb=" O ARG B 504 " (cutoff:3.500A) 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 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 700 Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.518A pdb=" N LEU B 710 " --> pdb=" O GLN B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.581A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 Processing helix chain 'B' and resid 806 through 811 removed outlier: 3.995A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.552A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.788A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.606A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) 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 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1175 through 1178 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 51 through 72 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 Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 188 through 193 removed outlier: 3.963A pdb=" N THR D 193 " --> pdb=" O ASP D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 199 removed outlier: 4.045A pdb=" N ASN D 199 " --> pdb=" O PRO D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing sheet with id=AA1, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.350A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.222A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 51 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.980A pdb=" N HIS C 131 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 111 through 113 removed outlier: 3.535A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.485A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AA7, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AA8, first strand: chain 'F' and resid 143 through 147 Processing sheet with id=AA9, first strand: chain 'G' and resid 37 through 39 removed outlier: 3.616A pdb=" N SER G 37 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 37 through 39 removed outlier: 3.616A pdb=" N SER G 37 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA G 76 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 86 through 93 removed outlier: 7.044A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY G 161 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.588A pdb=" N THR G 120 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR G 130 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 15 through 17 Processing sheet with id=AB5, first strand: chain 'I' and resid 44 through 47 removed outlier: 3.733A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A1149 " --> pdb=" O GLU A1196 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AB7, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AB8, first strand: chain 'L' and resid 37 through 40 removed outlier: 3.613A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 37 through 40 removed outlier: 3.613A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AC2, first strand: chain 'A' and resid 82 through 91 removed outlier: 10.755A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 10.633A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AC4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.755A pdb=" N LYS A 180 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 198 " --> pdb=" O TRP A 185 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 250 through 251 Processing sheet with id=AC6, first strand: chain 'A' and resid 343 through 345 Processing sheet with id=AC7, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.737A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 375 through 379 removed outlier: 5.972A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.586A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AD2, first strand: chain 'A' and resid 565 through 567 removed outlier: 6.149A pdb=" N VAL H 96 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.765A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AD5, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AD6, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AD7, first strand: chain 'A' and resid 1281 through 1292 removed outlier: 3.702A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 1141 through 1142 removed outlier: 6.517A pdb=" N THR A1141 " --> pdb=" O LEU A1273 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 69 through 73 removed outlier: 3.683A pdb=" N ARG B 86 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER B 156 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 150 through 151 removed outlier: 3.971A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 101 through 103 removed outlier: 3.886A pdb=" N HIS B 110 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AE4, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AE5, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.899A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AE7, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AE8, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.397A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.371A 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=AE9, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AF1, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 5.693A pdb=" N MET B 839 " --> pdb=" O ILE B 990 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B 992 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B1088 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AF3, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AF4, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AF5, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AF6, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AF7, first strand: chain 'D' and resid 36 through 38 1396 hydrogen bonds defined for protein. 3816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 9.36 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10700 1.34 - 1.46: 5653 1.46 - 1.58: 16803 1.58 - 1.70: 98 1.70 - 1.82: 290 Bond restraints: 33544 Sorted by residual: bond pdb=" P DG N 14 " pdb=" O5' DG N 14 " ideal model delta sigma weight residual 1.593 1.620 -0.027 1.00e-02 1.00e+04 7.52e+00 bond pdb=" C3' DC T 5 " pdb=" C2' DC T 5 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.84e+00 bond pdb=" C3' DC T 23 " pdb=" C2' DC T 23 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.77e+00 bond pdb=" N ASN A1390 " pdb=" CA ASN A1390 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.35e-02 5.49e+03 6.55e+00 bond pdb=" N1 DC N 6 " pdb=" C6 DC N 6 " ideal model delta sigma weight residual 1.367 1.352 0.015 6.00e-03 2.78e+04 5.99e+00 ... (remaining 33539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 44995 2.54 - 5.07: 415 5.07 - 7.61: 86 7.61 - 10.14: 10 10.14 - 12.68: 5 Bond angle restraints: 45511 Sorted by residual: angle pdb=" C GLN A 525 " pdb=" CA GLN A 525 " pdb=" CB GLN A 525 " ideal model delta sigma weight residual 116.63 109.53 7.10 1.16e+00 7.43e-01 3.74e+01 angle pdb=" CA PHE A1389 " pdb=" CB PHE A1389 " pdb=" CG PHE A1389 " ideal model delta sigma weight residual 113.80 119.22 -5.42 1.00e+00 1.00e+00 2.94e+01 angle pdb=" O5' DT T 20 " pdb=" C5' DT T 20 " pdb=" C4' DT T 20 " ideal model delta sigma weight residual 109.40 105.09 4.31 8.00e-01 1.56e+00 2.91e+01 angle pdb=" CA GLN A 525 " pdb=" C GLN A 525 " pdb=" N ASP A 526 " ideal model delta sigma weight residual 119.63 115.79 3.84 8.10e-01 1.52e+00 2.25e+01 angle pdb=" N3 DT T 6 " pdb=" C4 DT T 6 " pdb=" O4 DT T 6 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 45506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 20011 35.15 - 70.31: 406 70.31 - 105.46: 33 105.46 - 140.61: 0 140.61 - 175.76: 1 Dihedral angle restraints: 20451 sinusoidal: 8847 harmonic: 11604 Sorted by residual: 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 180.00 160.00 20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" C4' DA N 8 " pdb=" C3' DA N 8 " pdb=" O3' DA N 8 " pdb=" P DG N 9 " ideal model delta sinusoidal sigma weight residual -140.00 35.76 -175.76 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA GLN B 115 " pdb=" C GLN B 115 " pdb=" N GLU B 116 " pdb=" CA GLU B 116 " ideal model delta harmonic sigma weight residual 180.00 162.05 17.95 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 20448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 5038 0.128 - 0.257: 37 0.257 - 0.385: 3 0.385 - 0.513: 25 0.513 - 0.642: 13 Chirality restraints: 5116 Sorted by residual: chirality pdb=" P DT T 1 " pdb=" OP1 DT T 1 " pdb=" OP2 DT T 1 " pdb=" O5' DT T 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P DG N 9 " pdb=" OP1 DG N 9 " pdb=" OP2 DG N 9 " pdb=" O5' DG N 9 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.60 2.00e-01 2.50e+01 9.07e+00 chirality pdb=" P DG N 3 " pdb=" OP1 DG N 3 " pdb=" OP2 DG N 3 " pdb=" O5' DG N 3 " both_signs ideal model delta sigma weight residual True 2.34 2.93 -0.60 2.00e-01 2.50e+01 8.89e+00 ... (remaining 5113 not shown) Planarity restraints: 5724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 48 " -0.301 9.50e-02 1.11e+02 1.35e-01 1.13e+01 pdb=" NE ARG J 48 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG J 48 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG J 48 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG J 48 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " 0.050 5.00e-02 4.00e+02 7.50e-02 9.00e+00 pdb=" N PRO A 245 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1391 " 0.254 9.50e-02 1.11e+02 1.14e-01 8.06e+00 pdb=" NE ARG A1391 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A1391 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A1391 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1391 " 0.008 2.00e-02 2.50e+03 ... (remaining 5721 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 7 2.42 - 3.04: 19460 3.04 - 3.66: 50908 3.66 - 4.28: 79413 4.28 - 4.90: 129724 Nonbonded interactions: 279512 Sorted by model distance: nonbonded pdb=" O3' G P 20 " pdb="MG MG A1803 " model vdw 1.798 2.170 nonbonded pdb=" N7 DG T 13 " pdb="PT PT N 102 " model vdw 1.999 2.230 nonbonded pdb=" N7 DG N 5 " pdb="PT PT N 102 " model vdw 1.999 2.230 nonbonded pdb=" N1 DNH N 101 " pdb="PT PT N 102 " model vdw 2.027 2.230 nonbonded pdb=" N2 DNH N 101 " pdb="PT PT N 102 " model vdw 2.042 2.230 ... (remaining 279507 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: 2.200 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: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 37.760 Find NCS groups from input model: 0.160 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:7.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 : 0.003 0.041 33576 Z= 0.196 Angle : 0.669 16.382 45556 Z= 0.355 Chirality : 0.062 0.642 5116 Planarity : 0.005 0.135 5724 Dihedral : 14.085 175.764 12939 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.06 % Allowed : 0.09 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.13), residues: 3957 helix: 0.96 (0.14), residues: 1352 sheet: 0.20 (0.21), residues: 612 loop : -0.06 (0.14), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 48 TYR 0.036 0.001 TYR B 797 PHE 0.035 0.001 PHE A 444 TRP 0.038 0.002 TRP C 170 HIS 0.006 0.001 HIS A1387 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.20 (33544) covalent geometry : angle 0.64945 / 0.35 (45511) hydrogen bonds : bond 0.15989 / 10.78 ( 1438) hydrogen bonds : angle 7.05613 / 4.89 ( 3926) metal coordination : bond 0.00450 / 0.26 ( 32) metal coordination : angle 5.10424 / 3.16 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 633 time to evaluate : 1.315 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: G 3 PHE cc_start: 0.6570 (m-80) cc_final: 0.6276 (m-80) REVERT: G 51 TYR cc_start: 0.8021 (t80) cc_final: 0.7435 (t80) REVERT: A 706 HIS cc_start: 0.6802 (t-90) cc_final: 0.6525 (t-170) REVERT: A 873 MET cc_start: 0.8814 (mmp) cc_final: 0.8554 (mmp) REVERT: B 251 ILE cc_start: 0.6993 (mm) cc_final: 0.6780 (tp) REVERT: D 17 LYS cc_start: 0.5312 (mptt) cc_final: 0.4938 (mptt) REVERT: D 50 LEU cc_start: 0.6697 (tp) cc_final: 0.6373 (tp) REVERT: D 145 MET cc_start: 0.6909 (tpt) cc_final: 0.6673 (ppp) outliers start: 2 outliers final: 2 residues processed: 635 average time/residue: 0.8005 time to fit residues: 589.9256 Evaluate side-chains 380 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 378 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 381 MET Chi-restraints excluded: chain B residue 394 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 54 ASN G 10 ASN G 24 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 ASN I 89 GLN J 23 ASN J 53 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN A 584 ASN A1188 GLN A1278 ASN A1330 ASN B 309 GLN B 572 HIS B 686 ASN B 881 ASN B 932 HIS B1013 ASN B1141 HIS H 64 ASN H 83 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.121388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.084718 restraints weight = 48403.620| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.18 r_work: 0.3095 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 33576 Z= 0.234 Angle : 0.659 18.170 45556 Z= 0.341 Chirality : 0.047 0.280 5116 Planarity : 0.005 0.073 5724 Dihedral : 11.587 173.877 4948 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.16 % Allowed : 9.70 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.13), residues: 3957 helix: 1.01 (0.14), residues: 1363 sheet: 0.07 (0.20), residues: 628 loop : -0.04 (0.14), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 434 TYR 0.029 0.002 TYR B 797 PHE 0.029 0.002 PHE A 444 TRP 0.023 0.002 TRP C 170 HIS 0.006 0.001 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (33544) covalent geometry : angle 0.63862 / 0.34 (45511) hydrogen bonds : bond 0.04878 / 3.25 ( 1438) hydrogen bonds : angle 5.44526 / 3.79 ( 3926) metal coordination : bond 0.00684 / 0.44 ( 32) metal coordination : angle 5.23144 / 3.28 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 419 time to evaluate : 1.283 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: C 123 ASN cc_start: 0.8530 (t0) cc_final: 0.8281 (t0) REVERT: C 133 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8239 (mp) REVERT: C 152 GLU cc_start: 0.7688 (tp30) cc_final: 0.7474 (mm-30) REVERT: C 264 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7502 (tm-30) REVERT: E 87 SER cc_start: 0.8636 (t) cc_final: 0.8283 (p) REVERT: F 127 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8676 (pm20) REVERT: G 1 MET cc_start: 0.7029 (ttp) cc_final: 0.6624 (ttm) REVERT: G 51 TYR cc_start: 0.7761 (t80) cc_final: 0.6877 (t80) REVERT: G 69 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7137 (pt0) REVERT: I 11 ASN cc_start: 0.8330 (t0) cc_final: 0.8113 (t0) REVERT: I 15 TYR cc_start: 0.4298 (p90) cc_final: 0.2028 (p90) REVERT: I 54 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.5633 (pm20) REVERT: I 59 VAL cc_start: 0.8842 (m) cc_final: 0.8537 (p) REVERT: J 26 GLN cc_start: 0.8321 (tm-30) cc_final: 0.8021 (tm-30) REVERT: K 89 ASN cc_start: 0.8663 (m-40) cc_final: 0.8375 (m110) REVERT: L 47 ARG cc_start: 0.8400 (mtp85) cc_final: 0.7634 (mtp85) REVERT: A 124 GLN cc_start: 0.8871 (mt0) cc_final: 0.8291 (mm-40) REVERT: A 260 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8332 (t70) REVERT: A 281 HIS cc_start: 0.8686 (t-90) cc_final: 0.8427 (t-90) REVERT: A 706 HIS cc_start: 0.7409 (t-90) cc_final: 0.6988 (t70) REVERT: A 873 MET cc_start: 0.9302 (mmp) cc_final: 0.8976 (mmp) REVERT: A 1278 ASN cc_start: 0.7450 (OUTLIER) cc_final: 0.7177 (t0) REVERT: A 1281 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.6800 (tmm-80) REVERT: B 560 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7714 (pp20) REVERT: B 662 MET cc_start: 0.9050 (mmm) cc_final: 0.8770 (mmp) REVERT: D 60 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8384 (mmmt) REVERT: D 145 MET cc_start: 0.7682 (tpt) cc_final: 0.6909 (ppp) REVERT: H 123 MET cc_start: 0.9257 (ttp) cc_final: 0.9038 (ttt) REVERT: H 136 LYS cc_start: 0.8406 (mttm) cc_final: 0.7860 (mmtm) outliers start: 76 outliers final: 28 residues processed: 453 average time/residue: 0.7092 time to fit residues: 378.1026 Evaluate side-chains 410 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 375 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 54 GLU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1257 ASP Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1278 ASN Chi-restraints excluded: chain A residue 1281 ARG Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1451 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 198 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 226 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 249 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 32 GLN I 23 ASN J 23 ASN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN A 584 ASN A1278 ASN B 115 GLN B 309 GLN B 881 ASN B 932 HIS H 21 ASN H 64 ASN H 83 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.123072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.086783 restraints weight = 48004.351| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.17 r_work: 0.3137 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33576 Z= 0.128 Angle : 0.587 17.194 45556 Z= 0.302 Chirality : 0.044 0.257 5116 Planarity : 0.004 0.072 5724 Dihedral : 11.533 171.184 4945 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.54 % Allowed : 12.29 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.13), residues: 3957 helix: 1.17 (0.14), residues: 1367 sheet: 0.07 (0.20), residues: 635 loop : -0.02 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 153 TYR 0.021 0.001 TYR I 15 PHE 0.025 0.001 PHE A 219 TRP 0.014 0.001 TRP A1044 HIS 0.007 0.001 HIS D 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (33544) covalent geometry : angle 0.56402 / 0.30 (45511) hydrogen bonds : bond 0.04135 / 2.77 ( 1438) hydrogen bonds : angle 5.04744 / 3.52 ( 3926) metal coordination : bond 0.00467 / 0.28 ( 32) metal coordination : angle 5.15513 / 3.25 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 396 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8205 (mp) REVERT: C 152 GLU cc_start: 0.7617 (tp30) cc_final: 0.7303 (mm-30) REVERT: C 260 LEU cc_start: 0.8777 (tt) cc_final: 0.8573 (tt) REVERT: C 264 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7509 (tm-30) REVERT: E 87 SER cc_start: 0.8671 (t) cc_final: 0.8315 (p) REVERT: F 144 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8328 (mt-10) REVERT: G 1 MET cc_start: 0.6902 (ttp) cc_final: 0.5821 (ptp) REVERT: G 51 TYR cc_start: 0.7991 (t80) cc_final: 0.7041 (t80) REVERT: G 69 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7168 (pt0) REVERT: G 75 ARG cc_start: 0.8045 (mmt90) cc_final: 0.7639 (mmt90) REVERT: G 115 MET cc_start: 0.4950 (pmt) cc_final: 0.4478 (pmm) REVERT: I 11 ASN cc_start: 0.8240 (t0) cc_final: 0.8030 (t0) REVERT: I 54 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.5626 (pm20) REVERT: I 59 VAL cc_start: 0.8861 (m) cc_final: 0.8565 (p) REVERT: I 93 LYS cc_start: 0.8788 (mptp) cc_final: 0.8580 (tptt) REVERT: J 26 GLN cc_start: 0.8314 (tm-30) cc_final: 0.7998 (tm-30) REVERT: K 36 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7967 (mp0) REVERT: K 85 ASP cc_start: 0.8617 (m-30) cc_final: 0.8269 (m-30) REVERT: K 89 ASN cc_start: 0.8647 (m-40) cc_final: 0.8335 (m110) REVERT: L 28 LYS cc_start: 0.8380 (tppp) cc_final: 0.7816 (mmmt) REVERT: L 47 ARG cc_start: 0.8423 (mtp85) cc_final: 0.7535 (mtp85) REVERT: A 41 MET cc_start: 0.8265 (mmm) cc_final: 0.7399 (mmp) REVERT: A 124 GLN cc_start: 0.8860 (mt0) cc_final: 0.8280 (mm-40) REVERT: A 260 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8300 (t70) REVERT: A 281 HIS cc_start: 0.8667 (t-90) cc_final: 0.8363 (t-90) REVERT: A 706 HIS cc_start: 0.7368 (t-90) cc_final: 0.6984 (t70) REVERT: A 873 MET cc_start: 0.9257 (mmp) cc_final: 0.8847 (mmp) REVERT: A 1196 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7957 (mp0) REVERT: A 1297 GLU cc_start: 0.8684 (mp0) cc_final: 0.8390 (mp0) REVERT: B 251 ILE cc_start: 0.8029 (mm) cc_final: 0.7691 (tp) REVERT: B 354 ASP cc_start: 0.8430 (m-30) cc_final: 0.8074 (p0) REVERT: B 662 MET cc_start: 0.9040 (mmm) cc_final: 0.8753 (mmp) REVERT: D 57 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7797 (tt) REVERT: D 61 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8443 (mm-30) REVERT: D 145 MET cc_start: 0.7553 (tpt) cc_final: 0.6711 (ppp) REVERT: H 8 ASP cc_start: 0.8526 (t0) cc_final: 0.8302 (t0) REVERT: H 33 GLN cc_start: 0.7478 (mm-40) cc_final: 0.7242 (mt0) REVERT: H 105 GLU cc_start: 0.8020 (tt0) cc_final: 0.7621 (tt0) REVERT: H 136 LYS cc_start: 0.8433 (mttm) cc_final: 0.7939 (mmtm) outliers start: 54 outliers final: 21 residues processed: 422 average time/residue: 0.7668 time to fit residues: 384.6251 Evaluate side-chains 390 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 363 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 54 GLU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 924 LYS Chi-restraints excluded: chain A residue 931 GLU Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1257 ASP Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain H residue 54 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 242 optimal weight: 1.9990 chunk 332 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 138 optimal weight: 0.0970 chunk 208 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 340 optimal weight: 0.3980 chunk 324 optimal weight: 6.9990 chunk 367 optimal weight: 2.9990 chunk 369 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 32 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN B 932 HIS H 21 ASN H 64 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.122258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.085929 restraints weight = 47363.750| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.16 r_work: 0.3121 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33576 Z= 0.146 Angle : 0.567 17.229 45556 Z= 0.292 Chirality : 0.044 0.248 5116 Planarity : 0.004 0.072 5724 Dihedral : 11.495 173.265 4945 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.68 % Allowed : 13.74 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.13), residues: 3957 helix: 1.24 (0.14), residues: 1370 sheet: 0.06 (0.20), residues: 628 loop : 0.00 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 434 TYR 0.019 0.001 TYR E 46 PHE 0.026 0.001 PHE A 219 TRP 0.011 0.001 TRP A1044 HIS 0.004 0.001 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (33544) covalent geometry : angle 0.54703 / 0.29 (45511) hydrogen bonds : bond 0.03862 / 2.59 ( 1438) hydrogen bonds : angle 4.86657 / 3.40 ( 3926) metal coordination : bond 0.00486 / 0.32 ( 32) metal coordination : angle 4.78721 / 2.92 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 385 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8152 (mp) REVERT: C 152 GLU cc_start: 0.7723 (tp30) cc_final: 0.7470 (mm-30) REVERT: C 260 LEU cc_start: 0.8777 (tt) cc_final: 0.8571 (tt) REVERT: C 264 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7497 (tm-30) REVERT: E 9 ILE cc_start: 0.8494 (tt) cc_final: 0.8259 (tt) REVERT: G 51 TYR cc_start: 0.7896 (t80) cc_final: 0.6989 (t80) REVERT: G 75 ARG cc_start: 0.8159 (mmt90) cc_final: 0.7761 (mmt90) REVERT: I 11 ASN cc_start: 0.8278 (t0) cc_final: 0.8032 (t0) REVERT: I 54 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.5521 (pm20) REVERT: I 59 VAL cc_start: 0.8924 (m) cc_final: 0.8631 (p) REVERT: I 89 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8401 (mm110) REVERT: J 26 GLN cc_start: 0.8382 (tm-30) cc_final: 0.8055 (tm-30) REVERT: K 36 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7995 (mp0) REVERT: L 47 ARG cc_start: 0.8369 (mtp85) cc_final: 0.7478 (mtp85) REVERT: A 41 MET cc_start: 0.8276 (mmm) cc_final: 0.7577 (mmp) REVERT: A 47 ARG cc_start: 0.7765 (ttp-110) cc_final: 0.7533 (ttp-110) REVERT: A 124 GLN cc_start: 0.8850 (mt0) cc_final: 0.8288 (mm-40) REVERT: A 260 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8330 (t70) REVERT: A 281 HIS cc_start: 0.8675 (t-90) cc_final: 0.8343 (t-90) REVERT: A 706 HIS cc_start: 0.7381 (t-90) cc_final: 0.7000 (t70) REVERT: A 873 MET cc_start: 0.9271 (mmp) cc_final: 0.8877 (mmp) REVERT: A 1196 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: A 1209 MET cc_start: 0.8508 (mmm) cc_final: 0.8149 (mmm) REVERT: A 1278 ASN cc_start: 0.7664 (t0) cc_final: 0.7360 (t0) REVERT: A 1281 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6706 (tmm-80) REVERT: A 1297 GLU cc_start: 0.8725 (mp0) cc_final: 0.8418 (mp0) REVERT: B 354 ASP cc_start: 0.8406 (m-30) cc_final: 0.8072 (p0) REVERT: B 434 ARG cc_start: 0.7317 (ttp80) cc_final: 0.7114 (tmm-80) REVERT: B 662 MET cc_start: 0.9051 (mmm) cc_final: 0.8746 (mmp) REVERT: D 50 LEU cc_start: 0.7336 (tp) cc_final: 0.7130 (tp) REVERT: D 57 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7770 (tt) REVERT: D 61 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8451 (mm-30) REVERT: D 145 MET cc_start: 0.7493 (tpt) cc_final: 0.6604 (ppp) REVERT: D 213 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8445 (mm-30) REVERT: D 214 LEU cc_start: 0.8607 (pp) cc_final: 0.8265 (tm) REVERT: H 33 GLN cc_start: 0.7532 (mm-40) cc_final: 0.7297 (mt0) REVERT: H 106 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7501 (tm-30) REVERT: H 123 MET cc_start: 0.9210 (ttp) cc_final: 0.8972 (ttt) REVERT: H 136 LYS cc_start: 0.8482 (mttm) cc_final: 0.8086 (mmtm) outliers start: 59 outliers final: 28 residues processed: 412 average time/residue: 0.7685 time to fit residues: 375.5143 Evaluate side-chains 391 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 355 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 54 GLU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 417 TYR 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 727 ASP Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 931 GLU Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1257 ASP Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1281 ARG Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 106 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 64 optimal weight: 40.0000 chunk 247 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 274 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 306 optimal weight: 8.9990 chunk 297 optimal weight: 0.8980 chunk 198 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 54 GLN I 23 ASN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN B 115 GLN B 309 GLN B 878 GLN B 932 HIS D 34 GLN H 21 ASN H 64 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.120996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.084371 restraints weight = 46628.551| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.14 r_work: 0.3091 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33576 Z= 0.180 Angle : 0.580 17.270 45556 Z= 0.298 Chirality : 0.045 0.378 5116 Planarity : 0.004 0.071 5724 Dihedral : 11.439 175.519 4943 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.48 % Allowed : 13.66 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.13), residues: 3957 helix: 1.24 (0.14), residues: 1371 sheet: 0.06 (0.20), residues: 620 loop : 0.01 (0.14), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 119 TYR 0.022 0.001 TYR E 46 PHE 0.038 0.002 PHE D 70 TRP 0.009 0.001 TRP A1044 HIS 0.005 0.001 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (33544) covalent geometry : angle 0.56019 / 0.30 (45511) hydrogen bonds : bond 0.03912 / 2.62 ( 1438) hydrogen bonds : angle 4.82022 / 3.37 ( 3926) metal coordination : bond 0.00565 / 0.38 ( 32) metal coordination : angle 4.84912 / 3.03 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 374 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8211 (tpt) REVERT: C 133 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8077 (mp) REVERT: C 152 GLU cc_start: 0.7788 (tp30) cc_final: 0.7531 (tp30) REVERT: C 260 LEU cc_start: 0.8780 (tt) cc_final: 0.8573 (tt) REVERT: C 264 GLN cc_start: 0.7817 (tm-30) cc_final: 0.7546 (tm-30) REVERT: G 51 TYR cc_start: 0.7964 (t80) cc_final: 0.6974 (t80) REVERT: G 75 ARG cc_start: 0.8150 (mmt90) cc_final: 0.7782 (mmt90) REVERT: G 115 MET cc_start: 0.4858 (pmt) cc_final: 0.2923 (pmm) REVERT: I 11 ASN cc_start: 0.8269 (t0) cc_final: 0.8060 (t0) REVERT: I 54 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.5519 (pm20) REVERT: I 59 VAL cc_start: 0.8899 (m) cc_final: 0.8607 (p) REVERT: J 26 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8159 (tm-30) REVERT: K 36 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7990 (mp0) REVERT: K 89 ASN cc_start: 0.8635 (m110) cc_final: 0.8262 (m110) REVERT: L 47 ARG cc_start: 0.8351 (mtp85) cc_final: 0.7479 (mtp85) REVERT: A 41 MET cc_start: 0.8297 (mmm) cc_final: 0.7614 (mmp) REVERT: A 124 GLN cc_start: 0.8848 (mt0) cc_final: 0.8290 (mm-40) REVERT: A 260 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.8387 (t70) REVERT: A 281 HIS cc_start: 0.8655 (t-90) cc_final: 0.8374 (t-90) REVERT: A 706 HIS cc_start: 0.7352 (t-90) cc_final: 0.7035 (t70) REVERT: A 873 MET cc_start: 0.9296 (mmp) cc_final: 0.8912 (mmp) REVERT: A 1196 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: A 1278 ASN cc_start: 0.7630 (t0) cc_final: 0.7254 (t0) REVERT: A 1281 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.6710 (tmm-80) REVERT: A 1297 GLU cc_start: 0.8765 (mp0) cc_final: 0.8415 (mp0) REVERT: B 135 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7816 (mtm110) REVERT: B 354 ASP cc_start: 0.8361 (m-30) cc_final: 0.8079 (p0) REVERT: B 473 MET cc_start: 0.8129 (mpt) cc_final: 0.7897 (ptm) REVERT: B 662 MET cc_start: 0.9044 (mmm) cc_final: 0.8734 (mmp) REVERT: D 50 LEU cc_start: 0.7447 (tp) cc_final: 0.6978 (tp) REVERT: D 61 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8454 (mm-30) REVERT: D 145 MET cc_start: 0.7483 (tpt) cc_final: 0.6475 (tmm) REVERT: D 214 LEU cc_start: 0.8639 (pp) cc_final: 0.8285 (tm) REVERT: H 106 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: H 136 LYS cc_start: 0.8454 (mttm) cc_final: 0.8042 (mmtm) outliers start: 87 outliers final: 37 residues processed: 422 average time/residue: 0.7611 time to fit residues: 381.4559 Evaluate side-chains 392 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 348 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 54 GLU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 417 TYR 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 727 ASP Chi-restraints excluded: chain A residue 925 LEU Chi-restraints excluded: chain A residue 931 GLU Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1257 ASP Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1281 ARG Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 106 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 214 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 283 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 343 optimal weight: 2.9990 chunk 311 optimal weight: 1.9990 chunk 365 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 32 GLN I 89 GLN A 584 ASN B 115 GLN B 878 GLN B 932 HIS ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN H 64 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.121384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.084986 restraints weight = 46370.610| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.13 r_work: 0.3102 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33576 Z= 0.153 Angle : 0.573 17.077 45556 Z= 0.293 Chirality : 0.044 0.328 5116 Planarity : 0.004 0.071 5724 Dihedral : 11.448 176.431 4943 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.02 % Allowed : 15.05 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.13), residues: 3957 helix: 1.25 (0.14), residues: 1377 sheet: 0.06 (0.20), residues: 621 loop : 0.01 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 434 TYR 0.026 0.001 TYR E 46 PHE 0.025 0.001 PHE A 219 TRP 0.010 0.001 TRP A1044 HIS 0.005 0.001 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (33544) covalent geometry : angle 0.55358 / 0.29 (45511) hydrogen bonds : bond 0.03761 / 2.52 ( 1438) hydrogen bonds : angle 4.75895 / 3.33 ( 3926) metal coordination : bond 0.00495 / 0.33 ( 32) metal coordination : angle 4.72494 / 2.94 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 365 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8247 (tpt) REVERT: C 133 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8063 (mp) REVERT: C 152 GLU cc_start: 0.7792 (tp30) cc_final: 0.7523 (tp30) REVERT: C 260 LEU cc_start: 0.8809 (tt) cc_final: 0.8603 (tt) REVERT: C 264 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7556 (tm-30) REVERT: G 51 TYR cc_start: 0.7957 (t80) cc_final: 0.7022 (t80) REVERT: G 75 ARG cc_start: 0.8157 (mmt90) cc_final: 0.7782 (mmt90) REVERT: I 11 ASN cc_start: 0.8276 (t0) cc_final: 0.8029 (t0) REVERT: I 59 VAL cc_start: 0.8900 (m) cc_final: 0.8608 (p) REVERT: J 26 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8191 (tm-30) REVERT: K 36 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7995 (mp0) REVERT: K 89 ASN cc_start: 0.8638 (m110) cc_final: 0.8252 (m110) REVERT: L 47 ARG cc_start: 0.8373 (mtp85) cc_final: 0.7503 (mtp85) REVERT: A 41 MET cc_start: 0.8301 (mmm) cc_final: 0.7611 (mmp) REVERT: A 47 ARG cc_start: 0.7748 (ttp-110) cc_final: 0.7526 (ttp-110) REVERT: A 124 GLN cc_start: 0.8841 (mt0) cc_final: 0.8294 (mm-40) REVERT: A 281 HIS cc_start: 0.8657 (t-90) cc_final: 0.8359 (t-90) REVERT: A 453 MET cc_start: 0.8818 (mpp) cc_final: 0.8521 (mpp) REVERT: A 706 HIS cc_start: 0.7350 (t-90) cc_final: 0.6895 (t-90) REVERT: A 873 MET cc_start: 0.9294 (mmp) cc_final: 0.8862 (mmp) REVERT: A 1196 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: A 1209 MET cc_start: 0.8443 (mmm) cc_final: 0.8082 (mmm) REVERT: A 1218 GLN cc_start: 0.9213 (mm110) cc_final: 0.8906 (mm110) REVERT: A 1278 ASN cc_start: 0.7608 (t0) cc_final: 0.7217 (t0) REVERT: A 1281 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6671 (tmm-80) REVERT: A 1297 GLU cc_start: 0.8778 (mp0) cc_final: 0.8429 (mp0) REVERT: A 1398 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8989 (ttp) REVERT: B 135 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7832 (mtm110) REVERT: B 354 ASP cc_start: 0.8302 (m-30) cc_final: 0.8026 (p0) REVERT: B 434 ARG cc_start: 0.7312 (ttp80) cc_final: 0.7112 (tmm-80) REVERT: B 473 MET cc_start: 0.8110 (mpt) cc_final: 0.7890 (ptm) REVERT: B 662 MET cc_start: 0.9045 (mmm) cc_final: 0.8746 (mmp) REVERT: D 50 LEU cc_start: 0.7461 (tp) cc_final: 0.7080 (tp) REVERT: D 145 MET cc_start: 0.7527 (tpt) cc_final: 0.6484 (tmm) REVERT: D 214 LEU cc_start: 0.8640 (pp) cc_final: 0.8278 (tm) REVERT: H 19 ARG cc_start: 0.8942 (mtp180) cc_final: 0.8736 (mtp85) REVERT: H 106 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8057 (mm-30) REVERT: H 136 LYS cc_start: 0.8467 (mttm) cc_final: 0.7963 (mmtm) outliers start: 71 outliers final: 36 residues processed: 399 average time/residue: 0.7913 time to fit residues: 374.5809 Evaluate side-chains 396 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 354 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 47 ARG Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 417 TYR 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 931 GLU Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1257 ASP Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1281 ARG Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 106 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 149 optimal weight: 0.0170 chunk 24 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 350 optimal weight: 0.8980 chunk 335 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 chunk 318 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN A 584 ASN B 115 GLN B 932 HIS ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN H 21 ASN H 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.121218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.084707 restraints weight = 46416.064| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.13 r_work: 0.3090 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33576 Z= 0.171 Angle : 0.582 17.040 45556 Z= 0.297 Chirality : 0.044 0.334 5116 Planarity : 0.004 0.071 5724 Dihedral : 11.471 177.373 4943 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.05 % Allowed : 15.28 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.13), residues: 3957 helix: 1.24 (0.14), residues: 1377 sheet: 0.03 (0.21), residues: 623 loop : 0.01 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1199 TYR 0.027 0.001 TYR E 46 PHE 0.041 0.002 PHE D 70 TRP 0.010 0.001 TRP A1304 HIS 0.005 0.001 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (33544) covalent geometry : angle 0.56268 / 0.30 (45511) hydrogen bonds : bond 0.03781 / 2.53 ( 1438) hydrogen bonds : angle 4.74387 / 3.32 ( 3926) metal coordination : bond 0.00527 / 0.36 ( 32) metal coordination : angle 4.76107 / 2.97 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 371 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8273 (tpt) REVERT: C 133 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8063 (mp) REVERT: C 152 GLU cc_start: 0.7823 (tp30) cc_final: 0.7567 (tp30) REVERT: C 260 LEU cc_start: 0.8798 (tt) cc_final: 0.8589 (tt) REVERT: C 264 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7639 (tm-30) REVERT: E 25 ASP cc_start: 0.8317 (m-30) cc_final: 0.8075 (p0) REVERT: E 172 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7989 (tp30) REVERT: G 6 ASP cc_start: 0.6184 (OUTLIER) cc_final: 0.5035 (m-30) REVERT: G 51 TYR cc_start: 0.7958 (t80) cc_final: 0.6999 (t80) REVERT: G 75 ARG cc_start: 0.8078 (mmt90) cc_final: 0.7694 (mmt90) REVERT: G 115 MET cc_start: 0.4880 (pmt) cc_final: 0.2703 (pmm) REVERT: I 11 ASN cc_start: 0.8276 (t0) cc_final: 0.8035 (t0) REVERT: I 54 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.5565 (pm20) REVERT: I 59 VAL cc_start: 0.8916 (m) cc_final: 0.8632 (p) REVERT: I 89 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8366 (mm110) REVERT: J 26 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8225 (tm-30) REVERT: K 36 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8006 (mp0) REVERT: K 85 ASP cc_start: 0.8644 (m-30) cc_final: 0.8302 (m-30) REVERT: K 89 ASN cc_start: 0.8639 (m110) cc_final: 0.8255 (m110) REVERT: L 47 ARG cc_start: 0.8388 (mtp85) cc_final: 0.7494 (mtp85) REVERT: A 41 MET cc_start: 0.8288 (mmm) cc_final: 0.7600 (mmp) REVERT: A 47 ARG cc_start: 0.7748 (ttp-110) cc_final: 0.7519 (ttp-110) REVERT: A 124 GLN cc_start: 0.8877 (mt0) cc_final: 0.8351 (mm-40) REVERT: A 260 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8385 (t70) REVERT: A 281 HIS cc_start: 0.8630 (t-90) cc_final: 0.8313 (t-90) REVERT: A 706 HIS cc_start: 0.7418 (t-90) cc_final: 0.6990 (t-90) REVERT: A 873 MET cc_start: 0.9304 (mmp) cc_final: 0.8879 (mmp) REVERT: A 1196 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: A 1209 MET cc_start: 0.8416 (mmm) cc_final: 0.8093 (mmm) REVERT: A 1218 GLN cc_start: 0.9232 (mm110) cc_final: 0.8936 (mm110) REVERT: A 1237 ILE cc_start: 0.8930 (mm) cc_final: 0.8695 (mm) REVERT: A 1278 ASN cc_start: 0.7657 (t0) cc_final: 0.7214 (t0) REVERT: A 1297 GLU cc_start: 0.8788 (mp0) cc_final: 0.8432 (mp0) REVERT: A 1398 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.9016 (ttp) REVERT: B 135 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.7822 (mtm110) REVERT: B 354 ASP cc_start: 0.8300 (m-30) cc_final: 0.8033 (p0) REVERT: B 473 MET cc_start: 0.8124 (mpt) cc_final: 0.7878 (ptm) REVERT: B 662 MET cc_start: 0.9062 (mmm) cc_final: 0.8772 (mmp) REVERT: D 50 LEU cc_start: 0.7690 (tp) cc_final: 0.7388 (tp) REVERT: D 61 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8431 (mm-30) REVERT: D 145 MET cc_start: 0.7516 (tpt) cc_final: 0.6461 (tmm) REVERT: D 214 LEU cc_start: 0.8650 (pp) cc_final: 0.8278 (tm) REVERT: H 19 ARG cc_start: 0.8932 (mtp180) cc_final: 0.8715 (mtp85) REVERT: H 106 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8081 (mm-30) REVERT: H 136 LYS cc_start: 0.8486 (mttm) cc_final: 0.7985 (mmtm) outliers start: 72 outliers final: 37 residues processed: 410 average time/residue: 0.8138 time to fit residues: 393.2577 Evaluate side-chains 407 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 362 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 54 GLU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 47 ARG Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 417 TYR 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 931 GLU Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1257 ASP Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 106 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 219 optimal weight: 6.9990 chunk 325 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 284 optimal weight: 0.4980 chunk 177 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 584 ASN B 115 GLN B 932 HIS H 21 ASN H 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.120308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.083728 restraints weight = 45646.851| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.11 r_work: 0.3079 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 33576 Z= 0.205 Angle : 0.610 17.387 45556 Z= 0.311 Chirality : 0.045 0.242 5116 Planarity : 0.004 0.070 5724 Dihedral : 11.510 178.597 4943 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.96 % Allowed : 15.96 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.13), residues: 3957 helix: 1.17 (0.14), residues: 1377 sheet: -0.05 (0.21), residues: 627 loop : -0.01 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 209 TYR 0.028 0.002 TYR E 46 PHE 0.026 0.002 PHE A 219 TRP 0.010 0.001 TRP A 954 HIS 0.006 0.001 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (33544) covalent geometry : angle 0.58995 / 0.31 (45511) hydrogen bonds : bond 0.03919 / 2.63 ( 1438) hydrogen bonds : angle 4.78403 / 3.35 ( 3926) metal coordination : bond 0.00581 / 0.40 ( 32) metal coordination : angle 5.02074 / 3.18 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 381 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 GLU cc_start: 0.8081 (pm20) cc_final: 0.7860 (pm20) REVERT: C 133 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8057 (mp) REVERT: C 152 GLU cc_start: 0.7780 (tp30) cc_final: 0.7553 (tp30) REVERT: C 260 LEU cc_start: 0.8790 (tt) cc_final: 0.8577 (tt) REVERT: C 264 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7659 (tm-30) REVERT: E 25 ASP cc_start: 0.8372 (m-30) cc_final: 0.8127 (p0) REVERT: E 172 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8018 (tp30) REVERT: G 6 ASP cc_start: 0.6151 (OUTLIER) cc_final: 0.4927 (m-30) REVERT: G 51 TYR cc_start: 0.7967 (t80) cc_final: 0.7030 (t80) REVERT: G 75 ARG cc_start: 0.8068 (mmt90) cc_final: 0.7695 (mmt90) REVERT: G 115 MET cc_start: 0.4857 (pmt) cc_final: 0.4221 (pmm) REVERT: I 11 ASN cc_start: 0.8281 (t0) cc_final: 0.8040 (t0) REVERT: I 54 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.5487 (pm20) REVERT: I 59 VAL cc_start: 0.8901 (m) cc_final: 0.8620 (p) REVERT: J 26 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8249 (tm-30) REVERT: K 36 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8038 (mp0) REVERT: K 89 ASN cc_start: 0.8638 (m110) cc_final: 0.8246 (m110) REVERT: L 47 ARG cc_start: 0.8377 (mtp85) cc_final: 0.7506 (mtp85) REVERT: A 41 MET cc_start: 0.8285 (mmm) cc_final: 0.7609 (mmp) REVERT: A 124 GLN cc_start: 0.8876 (mt0) cc_final: 0.8352 (mm-40) REVERT: A 260 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8399 (t70) REVERT: A 281 HIS cc_start: 0.8664 (t-90) cc_final: 0.8322 (t-90) REVERT: A 706 HIS cc_start: 0.7439 (t-90) cc_final: 0.6970 (t-90) REVERT: A 873 MET cc_start: 0.9330 (mmp) cc_final: 0.8967 (mmp) REVERT: A 1196 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: A 1209 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8066 (mmm) REVERT: A 1218 GLN cc_start: 0.9237 (mm110) cc_final: 0.8935 (mm110) REVERT: A 1237 ILE cc_start: 0.8882 (mm) cc_final: 0.8666 (mm) REVERT: A 1278 ASN cc_start: 0.7604 (t0) cc_final: 0.7187 (t0) REVERT: A 1297 GLU cc_start: 0.8805 (mp0) cc_final: 0.8442 (mp0) REVERT: A 1398 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.9039 (ttp) REVERT: B 135 ARG cc_start: 0.8327 (ttm-80) cc_final: 0.7820 (mtm110) REVERT: B 354 ASP cc_start: 0.8291 (m-30) cc_final: 0.8034 (p0) REVERT: B 473 MET cc_start: 0.8113 (mpt) cc_final: 0.7878 (ptm) REVERT: B 662 MET cc_start: 0.9070 (mmm) cc_final: 0.8771 (mmp) REVERT: D 50 LEU cc_start: 0.7716 (tp) cc_final: 0.7261 (tp) REVERT: D 61 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8453 (mm-30) REVERT: D 145 MET cc_start: 0.7516 (tpt) cc_final: 0.6477 (tmm) REVERT: D 209 ARG cc_start: 0.8710 (ptm-80) cc_final: 0.8251 (ptm-80) REVERT: D 214 LEU cc_start: 0.8687 (pp) cc_final: 0.8314 (tm) REVERT: H 19 ARG cc_start: 0.8930 (mtp180) cc_final: 0.8698 (mtp85) REVERT: H 91 ASP cc_start: 0.9076 (m-30) cc_final: 0.8875 (m-30) REVERT: H 106 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8103 (mm-30) REVERT: H 126 GLU cc_start: 0.8717 (tt0) cc_final: 0.8491 (tt0) REVERT: H 136 LYS cc_start: 0.8490 (mttm) cc_final: 0.8065 (mmtm) outliers start: 69 outliers final: 40 residues processed: 416 average time/residue: 0.7755 time to fit residues: 380.4697 Evaluate side-chains 408 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 360 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 54 GLU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 47 ARG Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 417 TYR 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 931 GLU Chi-restraints excluded: chain A residue 1196 GLU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1257 ASP Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 106 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 116 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 330 optimal weight: 0.9980 chunk 396 optimal weight: 10.0000 chunk 64 optimal weight: 30.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 24 GLN A 311 GLN A 584 ASN A1330 ASN B 115 GLN B 932 HIS H 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.120248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.083606 restraints weight = 45807.689| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.12 r_work: 0.3079 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33576 Z= 0.186 Angle : 0.605 17.238 45556 Z= 0.309 Chirality : 0.045 0.242 5116 Planarity : 0.004 0.071 5724 Dihedral : 11.522 178.834 4943 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.93 % Allowed : 16.42 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.13), residues: 3957 helix: 1.15 (0.14), residues: 1380 sheet: -0.02 (0.21), residues: 624 loop : -0.01 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 434 TYR 0.031 0.001 TYR E 46 PHE 0.037 0.002 PHE D 70 TRP 0.010 0.001 TRP A 954 HIS 0.008 0.001 HIS A1124 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (33544) covalent geometry : angle 0.58520 / 0.31 (45511) hydrogen bonds : bond 0.03866 / 2.60 ( 1438) hydrogen bonds : angle 4.77762 / 3.34 ( 3926) metal coordination : bond 0.00571 / 0.39 ( 32) metal coordination : angle 4.91515 / 3.10 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 367 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 GLU cc_start: 0.8071 (pm20) cc_final: 0.7833 (pm20) REVERT: C 133 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8074 (mp) REVERT: C 152 GLU cc_start: 0.7850 (tp30) cc_final: 0.7531 (tp30) REVERT: C 260 LEU cc_start: 0.8781 (tt) cc_final: 0.8570 (tt) REVERT: C 264 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7655 (tm-30) REVERT: E 25 ASP cc_start: 0.8365 (m-30) cc_final: 0.8125 (p0) REVERT: E 172 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8116 (tt0) REVERT: E 198 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.7983 (mm) REVERT: G 6 ASP cc_start: 0.6154 (OUTLIER) cc_final: 0.4880 (m-30) REVERT: G 24 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7695 (pt0) REVERT: G 51 TYR cc_start: 0.7980 (t80) cc_final: 0.7144 (t80) REVERT: G 75 ARG cc_start: 0.8046 (mmt90) cc_final: 0.7669 (mmt90) REVERT: G 115 MET cc_start: 0.4875 (pmt) cc_final: 0.4281 (pmm) REVERT: I 11 ASN cc_start: 0.8270 (t0) cc_final: 0.8030 (t0) REVERT: I 54 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.5476 (pm20) REVERT: I 59 VAL cc_start: 0.8903 (m) cc_final: 0.8624 (p) REVERT: J 26 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8267 (tm-30) REVERT: K 36 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8032 (mp0) REVERT: L 47 ARG cc_start: 0.8383 (mtp85) cc_final: 0.7499 (mtp85) REVERT: A 41 MET cc_start: 0.8268 (mmm) cc_final: 0.7577 (mmp) REVERT: A 63 ARG cc_start: 0.8510 (mtm110) cc_final: 0.7722 (tpm170) REVERT: A 124 GLN cc_start: 0.8872 (mt0) cc_final: 0.8340 (mm-40) REVERT: A 260 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8410 (t70) REVERT: A 281 HIS cc_start: 0.8680 (t-90) cc_final: 0.8341 (t-90) REVERT: A 706 HIS cc_start: 0.7500 (t-90) cc_final: 0.7020 (t-90) REVERT: A 748 MET cc_start: 0.8908 (mtt) cc_final: 0.8602 (mtt) REVERT: A 771 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8247 (mt-10) REVERT: A 873 MET cc_start: 0.9327 (mmp) cc_final: 0.8907 (mmp) REVERT: A 1196 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: A 1209 MET cc_start: 0.8408 (mmm) cc_final: 0.8063 (mmm) REVERT: A 1218 GLN cc_start: 0.9263 (mm110) cc_final: 0.8952 (mm110) REVERT: A 1237 ILE cc_start: 0.8864 (mm) cc_final: 0.8644 (mm) REVERT: A 1278 ASN cc_start: 0.7598 (t0) cc_final: 0.7145 (t0) REVERT: A 1297 GLU cc_start: 0.8799 (mp0) cc_final: 0.8428 (mp0) REVERT: A 1398 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.9012 (ttp) REVERT: B 135 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.7816 (mtm110) REVERT: B 354 ASP cc_start: 0.8275 (m-30) cc_final: 0.8022 (p0) REVERT: B 434 ARG cc_start: 0.7191 (ttp80) cc_final: 0.6730 (tmm-80) REVERT: B 473 MET cc_start: 0.8105 (mpt) cc_final: 0.7883 (ptm) REVERT: B 531 GLN cc_start: 0.8828 (mt0) cc_final: 0.8552 (mt0) REVERT: B 662 MET cc_start: 0.9054 (mmm) cc_final: 0.8772 (mmp) REVERT: D 50 LEU cc_start: 0.7674 (tp) cc_final: 0.7173 (tp) REVERT: D 61 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8439 (mm-30) REVERT: D 145 MET cc_start: 0.7513 (tpt) cc_final: 0.6471 (tmm) REVERT: D 213 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8652 (mp0) REVERT: H 11 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8525 (tt0) REVERT: H 19 ARG cc_start: 0.8922 (mtp180) cc_final: 0.8681 (mtp85) REVERT: H 106 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8114 (mm-30) REVERT: H 126 GLU cc_start: 0.8715 (tt0) cc_final: 0.8482 (tt0) REVERT: H 136 LYS cc_start: 0.8487 (mttm) cc_final: 0.8058 (mmtm) outliers start: 68 outliers final: 41 residues processed: 403 average time/residue: 0.7728 time to fit residues: 367.7314 Evaluate side-chains 412 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 360 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 54 GLU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain K residue 47 ARG Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 417 TYR 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 1196 GLU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1257 ASP Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 106 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 303 optimal weight: 0.9990 chunk 390 optimal weight: 0.0070 chunk 96 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 chunk 200 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 357 optimal weight: 3.9990 chunk 260 optimal weight: 5.9990 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 24 GLN A 584 ASN A1330 ASN B 115 GLN B 932 HIS D 34 GLN H 52 GLN H 64 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.121436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.084978 restraints weight = 46298.599| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.13 r_work: 0.3104 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33576 Z= 0.136 Angle : 0.597 16.447 45556 Z= 0.303 Chirality : 0.044 0.241 5116 Planarity : 0.004 0.071 5724 Dihedral : 11.503 178.743 4943 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.39 % Allowed : 17.01 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.13), residues: 3957 helix: 1.20 (0.14), residues: 1381 sheet: 0.01 (0.21), residues: 624 loop : -0.02 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 153 TYR 0.028 0.001 TYR E 46 PHE 0.036 0.001 PHE D 154 TRP 0.011 0.001 TRP C 201 HIS 0.007 0.001 HIS A1124 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (33544) covalent geometry : angle 0.57870 / 0.30 (45511) hydrogen bonds : bond 0.03673 / 2.47 ( 1438) hydrogen bonds : angle 4.71071 / 3.29 ( 3926) metal coordination : bond 0.00462 / 0.31 ( 32) metal coordination : angle 4.63884 / 2.91 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7914 Ramachandran restraints generated. 3957 Oldfield, 0 Emsley, 3957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 381 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 GLU cc_start: 0.8076 (pm20) cc_final: 0.7824 (pm20) REVERT: C 133 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8024 (mp) REVERT: C 152 GLU cc_start: 0.7809 (tp30) cc_final: 0.7474 (tp30) REVERT: C 260 LEU cc_start: 0.8823 (tt) cc_final: 0.8616 (tt) REVERT: C 264 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7658 (tm-30) REVERT: E 25 ASP cc_start: 0.8395 (m-30) cc_final: 0.8178 (p0) REVERT: E 172 GLU cc_start: 0.8246 (mm-30) cc_final: 0.8039 (tt0) REVERT: E 198 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.7913 (mm) REVERT: G 6 ASP cc_start: 0.6186 (OUTLIER) cc_final: 0.5319 (m-30) REVERT: G 21 ARG cc_start: 0.8387 (ptp-110) cc_final: 0.8041 (ptp-110) REVERT: G 51 TYR cc_start: 0.7948 (t80) cc_final: 0.7017 (t80) REVERT: G 75 ARG cc_start: 0.8070 (mmt90) cc_final: 0.7772 (mmt90) REVERT: G 115 MET cc_start: 0.4885 (pmt) cc_final: 0.4512 (pmm) REVERT: I 11 ASN cc_start: 0.8267 (t0) cc_final: 0.7993 (t0) REVERT: I 54 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.5443 (pm20) REVERT: I 59 VAL cc_start: 0.8893 (m) cc_final: 0.8623 (p) REVERT: J 26 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8295 (tm-30) REVERT: K 36 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8026 (mp0) REVERT: K 89 ASN cc_start: 0.8614 (m110) cc_final: 0.8259 (m110) REVERT: L 47 ARG cc_start: 0.8391 (mtp85) cc_final: 0.7510 (mtp85) REVERT: A 41 MET cc_start: 0.8283 (mmm) cc_final: 0.7609 (mmp) REVERT: A 63 ARG cc_start: 0.8456 (mtm110) cc_final: 0.7671 (tpm170) REVERT: A 124 GLN cc_start: 0.8855 (mt0) cc_final: 0.8338 (mm-40) REVERT: A 260 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8374 (t70) REVERT: A 281 HIS cc_start: 0.8694 (t-90) cc_final: 0.8354 (t-90) REVERT: A 706 HIS cc_start: 0.7598 (t-90) cc_final: 0.7183 (t-90) REVERT: A 771 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8217 (mt-10) REVERT: A 873 MET cc_start: 0.9290 (mmp) cc_final: 0.8865 (mmp) REVERT: A 1196 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: A 1209 MET cc_start: 0.8381 (mmm) cc_final: 0.8045 (mmm) REVERT: A 1218 GLN cc_start: 0.9262 (mm110) cc_final: 0.8939 (mm110) REVERT: A 1237 ILE cc_start: 0.8846 (mm) cc_final: 0.8627 (mm) REVERT: A 1278 ASN cc_start: 0.7612 (t0) cc_final: 0.7215 (t0) REVERT: A 1297 GLU cc_start: 0.8788 (mp0) cc_final: 0.8433 (mp0) REVERT: A 1398 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.9010 (ttp) REVERT: B 135 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.8017 (ttm-80) REVERT: B 326 ASP cc_start: 0.7984 (t70) cc_final: 0.7456 (t70) REVERT: B 354 ASP cc_start: 0.8267 (m-30) cc_final: 0.8009 (p0) REVERT: B 434 ARG cc_start: 0.7225 (ttp80) cc_final: 0.6748 (tmm-80) REVERT: B 473 MET cc_start: 0.8107 (mpt) cc_final: 0.7889 (ptm) REVERT: B 531 GLN cc_start: 0.8802 (mt0) cc_final: 0.8537 (mt0) REVERT: B 595 ARG cc_start: 0.8249 (ttp-110) cc_final: 0.8013 (ttp-110) REVERT: B 662 MET cc_start: 0.9062 (mmm) cc_final: 0.8776 (mmp) REVERT: B 1206 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8684 (mt-10) REVERT: D 50 LEU cc_start: 0.7692 (tp) cc_final: 0.7384 (tp) REVERT: D 60 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8696 (mmpt) REVERT: D 61 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8426 (mm-30) REVERT: D 145 MET cc_start: 0.7505 (tpt) cc_final: 0.6511 (tmm) REVERT: D 213 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8568 (mp0) REVERT: D 214 LEU cc_start: 0.8489 (pp) cc_final: 0.8149 (tm) REVERT: H 19 ARG cc_start: 0.8938 (mtp180) cc_final: 0.8698 (mtp85) REVERT: H 91 ASP cc_start: 0.9089 (m-30) cc_final: 0.8860 (m-30) REVERT: H 106 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8110 (mm-30) REVERT: H 126 GLU cc_start: 0.8716 (tt0) cc_final: 0.8497 (tt0) REVERT: H 136 LYS cc_start: 0.8490 (mttm) cc_final: 0.8064 (mmtm) outliers start: 49 outliers final: 30 residues processed: 403 average time/residue: 0.7657 time to fit residues: 365.5525 Evaluate side-chains 400 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 361 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 54 GLU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 417 TYR 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 1196 GLU Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1257 ASP Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain H residue 106 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 385 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 89 optimal weight: 0.0040 chunk 3 optimal weight: 0.6980 chunk 106 optimal weight: 40.0000 chunk 2 optimal weight: 3.9990 chunk 382 optimal weight: 8.9990 chunk 194 optimal weight: 0.6980 chunk 267 optimal weight: 0.6980 chunk 388 optimal weight: 5.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 24 GLN A 584 ASN A1330 ASN B 115 GLN B 932 HIS D 34 GLN H 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.121543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.085121 restraints weight = 46030.898| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.13 r_work: 0.3108 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33576 Z= 0.133 Angle : 0.585 16.060 45556 Z= 0.296 Chirality : 0.044 0.239 5116 Planarity : 0.004 0.071 5724 Dihedral : 11.477 179.002 4943 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.42 % Allowed : 17.24 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.14), residues: 3957 helix: 1.24 (0.14), residues: 1383 sheet: 0.04 (0.21), residues: 615 loop : -0.01 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 209 TYR 0.030 0.001 TYR E 46 PHE 0.030 0.001 PHE D 154 TRP 0.011 0.001 TRP A1044 HIS 0.007 0.001 HIS A1124 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (33544) covalent geometry : angle 0.56769 / 0.30 (45511) hydrogen bonds : bond 0.03580 / 2.41 ( 1438) hydrogen bonds : angle 4.67341 / 3.27 ( 3926) metal coordination : bond 0.00454 / 0.30 ( 32) metal coordination : angle 4.47175 / 2.78 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15818.02 seconds wall clock time: 269 minutes 21.40 seconds (16161.40 seconds total)