Starting phenix.real_space_refine on Mon Sep 14 20:51:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6k4y_9916/09_2026/6k4y_9916.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k4y_9916/09_2026/6k4y_9916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6k4y_9916/09_2026/6k4y_9916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k4y_9916/09_2026/6k4y_9916.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6k4y_9916/09_2026/6k4y_9916.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6k4y_9916/09_2026/6k4y_9916.cif" model { file = "/net/cci-nas-00/data/ceres_data/6k4y_9916/09_2026/6k4y_9916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k4y_9916/09_2026/6k4y_9916.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 105 5.49 5 Mg 1 5.21 5 S 137 5.16 5 C 20536 2.51 5 N 5884 2.21 5 O 6582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33247 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1686 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1673 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1282} Chain: "D" Number of atoms: 10384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10384 Classifications: {'peptide': 1335} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1279} Chain breaks: 2 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 3781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3781 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 14, 'TRANS': 448} Chain breaks: 3 Chain: "I" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 729 Classifications: {'peptide': 88} Link IDs: {'TRANS': 87} Chain: "M" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1638 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 205} Chain: "N" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1223 Classifications: {'DNA': 59} Link IDs: {'rna3p': 58} Chain: "T" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 936 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain breaks: 1 Chain: "D" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14375 SG CYS D 70 112.221 80.164 69.021 1.00246.10 S ATOM 14521 SG CYS D 88 113.627 83.179 67.558 1.00234.97 S ATOM 20209 SG CYS D 814 80.053 100.736 127.254 1.00129.78 S ATOM 20774 SG CYS D 888 80.127 100.167 122.633 1.00124.84 S ATOM 20825 SG CYS D 895 79.376 97.507 124.881 1.00118.99 S ATOM 20846 SG CYS D 898 77.013 100.142 125.450 1.00116.34 S Time building chain proxies: 6.88, per 1000 atoms: 0.21 Number of scatterers: 33247 At special positions: 0 Unit cell: (171.217, 190.822, 160.761, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 137 16.00 P 105 15.00 Mg 1 11.99 O 6582 8.00 N 5884 7.00 C 20536 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: 2.82 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " Number of angles added : 6 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7340 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 55 sheets defined 43.3% alpha, 13.4% beta 45 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 4.12 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.608A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.727A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.975A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.756A pdb=" N LEU B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 212 through 227 removed outlier: 3.620A pdb=" N ALA B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 removed outlier: 3.647A pdb=" N PHE B 231 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 232' Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.584A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.642A pdb=" N CYS C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.622A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 removed outlier: 3.788A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.635A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.629A pdb=" N THR C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.676A pdb=" N ALA C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 387 Processing helix chain 'C' and resid 398 through 409 removed outlier: 3.547A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.801A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 482 removed outlier: 4.193A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 507 removed outlier: 3.592A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.771A pdb=" N GLY C 612 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.595A pdb=" N GLN C 659 " --> pdb=" O SER C 656 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 661 " --> pdb=" O GLN C 658 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 656 through 661' Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.596A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 Processing helix chain 'C' and resid 896 through 905 Processing helix chain 'C' and resid 943 through 979 Processing helix chain 'C' and resid 993 through 998 removed outlier: 3.654A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.883A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.658A pdb=" N THR C1115 " --> pdb=" O GLN C1111 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.886A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1176 Processing helix chain 'C' and resid 1177 through 1179 No H-bonds generated for 'chain 'C' and resid 1177 through 1179' Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.534A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.557A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.580A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1290 removed outlier: 3.844A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.534A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.609A pdb=" N SER D 34 " --> pdb=" O ILE D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 95 through 100 removed outlier: 3.724A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 100 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.571A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 236 removed outlier: 3.672A pdb=" N TRP D 236 " --> pdb=" O LYS D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 removed outlier: 4.079A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.564A pdb=" N MET D 330 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 342 removed outlier: 3.757A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 407 through 415 removed outlier: 3.677A pdb=" N ILE D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 removed outlier: 4.059A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.562A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 613 removed outlier: 3.656A pdb=" N GLY D 613 " --> pdb=" O TYR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.678A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 669 Processing helix chain 'D' and resid 675 through 702 Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 741 removed outlier: 4.018A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.838A pdb=" N TYR D 772 " --> pdb=" O ASN D 768 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 805 " --> pdb=" O VAL D 801 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.833A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.674A pdb=" N SER D 887 " --> pdb=" O SER D 884 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 899 No H-bonds generated for 'chain 'D' and resid 897 through 899' Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.807A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 removed outlier: 3.574A pdb=" N LEU D 930 " --> pdb=" O GLY D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1069 through 1074 removed outlier: 3.880A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU D1074 " --> pdb=" O GLY D1070 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1069 through 1074' Processing helix chain 'D' and resid 1137 through 1147 removed outlier: 3.648A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.692A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 3.970A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1251 through 1261 removed outlier: 3.646A pdb=" N LEU D1261 " --> pdb=" O VAL D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1281 through 1292 Processing helix chain 'D' and resid 1310 through 1315 removed outlier: 4.021A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1325 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.776A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1360 through 1372 removed outlier: 4.185A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.539A pdb=" N VAL E 10 " --> pdb=" O VAL E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 32 removed outlier: 3.505A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 80 removed outlier: 4.561A pdb=" N LEU E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 112 through 136 Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.733A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 234 removed outlier: 4.174A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 257 Processing helix chain 'F' and resid 262 through 293 Processing helix chain 'F' and resid 299 through 304 Processing helix chain 'F' and resid 313 through 321 Processing helix chain 'F' and resid 324 through 329 Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 333 through 352 removed outlier: 4.222A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 392 removed outlier: 5.481A pdb=" N ARG F 385 " --> pdb=" O GLU F 381 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS F 392 " --> pdb=" O ILE F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 400 through 417 removed outlier: 3.765A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 447 removed outlier: 4.330A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 475 Processing helix chain 'F' and resid 479 through 487 Processing helix chain 'F' and resid 491 through 500 removed outlier: 3.569A pdb=" N ARG F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS F 496 " --> pdb=" O ASP F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 515 removed outlier: 3.820A pdb=" N GLU F 515 " --> pdb=" O GLY F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 522 Processing helix chain 'F' and resid 541 through 551 removed outlier: 3.529A pdb=" N VAL F 547 " --> pdb=" O ALA F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 561 Processing helix chain 'F' and resid 572 through 597 removed outlier: 4.128A pdb=" N ARG F 596 " --> pdb=" O ALA F 592 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS F 597 " --> pdb=" O LYS F 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 608 removed outlier: 3.874A pdb=" N LEU F 607 " --> pdb=" O ARG F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 609 through 611 No H-bonds generated for 'chain 'F' and resid 609 through 611' Processing helix chain 'I' and resid 4 through 21 Processing helix chain 'I' and resid 24 through 29 removed outlier: 4.245A pdb=" N GLU I 28 " --> pdb=" O GLU I 24 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 24 through 29' Processing helix chain 'I' and resid 30 through 41 Processing helix chain 'I' and resid 50 through 60 Processing helix chain 'I' and resid 62 through 74 Processing helix chain 'I' and resid 77 through 87 removed outlier: 3.633A pdb=" N TYR I 81 " --> pdb=" O PHE I 77 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR I 83 " --> pdb=" O GLY I 79 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR I 87 " --> pdb=" O TYR I 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 11 Processing helix chain 'M' and resid 16 through 29 Processing helix chain 'M' and resid 33 through 40 Processing helix chain 'M' and resid 45 through 59 Processing helix chain 'M' and resid 72 through 90 Processing helix chain 'M' and resid 107 through 124 Processing helix chain 'M' and resid 168 through 178 removed outlier: 3.952A pdb=" N ILE M 178 " --> pdb=" O LYS M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 209 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 6.710A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 104 removed outlier: 6.060A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.936A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 17 removed outlier: 4.367A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 15 through 17 removed outlier: 4.367A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AB2, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AB3, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.548A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.865A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.671A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB7, first strand: chain 'C' and resid 451 through 453 removed outlier: 6.462A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB9, first strand: chain 'C' and resid 226 through 231 removed outlier: 4.774A pdb=" N GLU C 226 " --> pdb=" O PHE C 337 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AC2, first strand: chain 'C' and resid 249 through 250 removed outlier: 4.166A pdb=" N GLU C 249 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.747A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.237A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 301 through 302 removed outlier: 7.163A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.598A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.598A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 716 through 718 removed outlier: 6.654A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP C 781 " --> pdb=" O ALA C 718 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 722 through 727 removed outlier: 5.383A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.694A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AD3, first strand: chain 'C' and resid 1079 through 1080 removed outlier: 7.019A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 830 through 838 removed outlier: 3.938A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 876 through 877 Processing sheet with id=AD6, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.791A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD8, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.200A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.815A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.544A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1335 through 1339 removed outlier: 3.780A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP D1342 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 103 through 112 removed outlier: 10.430A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.496A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AE5, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AE6, first strand: chain 'D' and resid 526 through 527 removed outlier: 7.583A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.317A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE9, first strand: chain 'D' and resid 825 through 826 removed outlier: 6.738A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.451A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 949 through 952 removed outlier: 6.763A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 957 through 959 Processing sheet with id=AF4, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AF5, first strand: chain 'D' and resid 1025 through 1026 Processing sheet with id=AF6, first strand: chain 'D' and resid 1098 through 1100 removed outlier: 3.636A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 1046 through 1050 removed outlier: 3.787A pdb=" N ALA D1105 " --> pdb=" O VAL D1061 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 1190 through 1191 removed outlier: 6.784A pdb=" N LYS D1172 " --> pdb=" O GLU D1168 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLU D1168 " --> pdb=" O LYS D1172 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG D1174 " --> pdb=" O GLY D1166 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D1204 " --> pdb=" O GLY D1161 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 1264 through 1268 removed outlier: 6.848A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 128 through 133 removed outlier: 7.248A pdb=" N ILE M 141 " --> pdb=" O LYS M 129 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL M 131 " --> pdb=" O LEU M 139 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU M 139 " --> pdb=" O VAL M 131 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ARG M 150 " --> pdb=" O LEU M 142 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE M 149 " --> pdb=" O TYR M 165 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N TYR M 165 " --> pdb=" O ILE M 149 " (cutoff:3.500A) 1369 hydrogen bonds defined for protein. 3870 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 106 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 9.59 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8774 1.33 - 1.45: 6151 1.45 - 1.57: 18573 1.57 - 1.69: 207 1.69 - 1.81: 242 Bond restraints: 33947 Sorted by residual: bond pdb=" C3' DA T 28 " pdb=" C2' DA T 28 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DA T 37 " pdb=" C2' DA T 37 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" N9 DA T 40 " pdb=" C4 DA T 40 " ideal model delta sigma weight residual 1.374 1.355 0.019 6.00e-03 2.78e+04 1.03e+01 bond pdb=" C3' DA T 31 " pdb=" O3' DA T 31 " ideal model delta sigma weight residual 1.435 1.395 0.040 1.30e-02 5.92e+03 9.53e+00 bond pdb=" C3' DT N 18 " pdb=" O3' DT N 18 " ideal model delta sigma weight residual 1.435 1.396 0.039 1.30e-02 5.92e+03 9.18e+00 ... (remaining 33942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 44564 2.34 - 4.68: 1487 4.68 - 7.03: 163 7.03 - 9.37: 35 9.37 - 11.71: 9 Bond angle restraints: 46258 Sorted by residual: angle pdb=" C ILE I 26 " pdb=" N VAL I 27 " pdb=" CA VAL I 27 " ideal model delta sigma weight residual 122.66 115.35 7.31 9.70e-01 1.06e+00 5.69e+01 angle pdb=" N VAL I 27 " pdb=" CA VAL I 27 " pdb=" C VAL I 27 " ideal model delta sigma weight residual 111.90 106.47 5.43 8.10e-01 1.52e+00 4.50e+01 angle pdb=" C ARG D 709 " pdb=" N ASP D 710 " pdb=" CA ASP D 710 " ideal model delta sigma weight residual 121.54 133.25 -11.71 1.91e+00 2.74e-01 3.76e+01 angle pdb=" C LYS M 102 " pdb=" N ALA M 103 " pdb=" CA ALA M 103 " ideal model delta sigma weight residual 121.70 132.72 -11.02 1.80e+00 3.09e-01 3.75e+01 angle pdb=" C SER B 20 " pdb=" N SER B 21 " pdb=" CA SER B 21 " ideal model delta sigma weight residual 121.54 132.11 -10.57 1.91e+00 2.74e-01 3.06e+01 ... (remaining 46253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.61: 19597 28.61 - 57.21: 974 57.21 - 85.82: 91 85.82 - 114.42: 3 114.42 - 143.03: 2 Dihedral angle restraints: 20667 sinusoidal: 9287 harmonic: 11380 Sorted by residual: dihedral pdb=" CA VAL A 192 " pdb=" C VAL A 192 " pdb=" N GLU A 193 " pdb=" CA GLU A 193 " ideal model delta harmonic sigma weight residual -180.00 -150.79 -29.21 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA LYS C1133 " pdb=" C LYS C1133 " pdb=" N GLN C1134 " pdb=" CA GLN C1134 " ideal model delta harmonic sigma weight residual 180.00 151.55 28.45 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual -180.00 -151.84 -28.16 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 20664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3996 0.063 - 0.126: 1090 0.126 - 0.190: 166 0.190 - 0.253: 22 0.253 - 0.316: 8 Chirality restraints: 5282 Sorted by residual: chirality pdb=" CB ILE C 39 " pdb=" CA ILE C 39 " pdb=" CG1 ILE C 39 " pdb=" CG2 ILE C 39 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CB ILE C 854 " pdb=" CA ILE C 854 " pdb=" CG1 ILE C 854 " pdb=" CG2 ILE C 854 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA ASP D 710 " pdb=" N ASP D 710 " pdb=" C ASP D 710 " pdb=" CB ASP D 710 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 5279 not shown) Planarity restraints: 5664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 20 " -0.016 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C SER B 20 " 0.060 2.00e-02 2.50e+03 pdb=" O SER B 20 " -0.024 2.00e-02 2.50e+03 pdb=" N SER B 21 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 708 " 0.018 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C ASN D 708 " -0.059 2.00e-02 2.50e+03 pdb=" O ASN D 708 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG D 709 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 25 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C ASP I 25 " 0.059 2.00e-02 2.50e+03 pdb=" O ASP I 25 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE I 26 " -0.020 2.00e-02 2.50e+03 ... (remaining 5661 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 7164 2.77 - 3.31: 30662 3.31 - 3.84: 56281 3.84 - 4.37: 64373 4.37 - 4.90: 105190 Nonbonded interactions: 263670 Sorted by model distance: nonbonded pdb=" OG1 THR D1029 " pdb=" O SER D1116 " model vdw 2.242 3.040 nonbonded pdb=" O2 DC N 27 " pdb=" N2 DG T 35 " model vdw 2.245 2.496 nonbonded pdb=" O ARG C1033 " pdb=" OG1 THR C1037 " model vdw 2.256 3.040 nonbonded pdb=" OG1 THR D 514 " pdb=" O GLN D 594 " model vdw 2.261 3.040 nonbonded pdb=" O ASP F 278 " pdb=" OG1 THR F 282 " model vdw 2.267 3.040 ... (remaining 263665 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 232)) selection = (chain 'B' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 232)) } 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 group one per residue 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: 0.560 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: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 39.770 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 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 : 0.008 0.217 33953 Z= 0.415 Angle : 1.018 31.599 46264 Z= 0.598 Chirality : 0.058 0.316 5282 Planarity : 0.007 0.073 5664 Dihedral : 15.111 143.028 13327 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.60 % Favored : 92.30 % Rotamer: Outliers : 0.68 % Allowed : 5.05 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.54 (0.10), residues: 3920 helix: -3.13 (0.09), residues: 1530 sheet: -2.52 (0.22), residues: 432 loop : -3.02 (0.11), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 270 TYR 0.025 0.003 TYR A 177 PHE 0.040 0.003 PHE D 620 TRP 0.030 0.003 TRP C 183 HIS 0.012 0.002 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00768 / 0.41 (33947) covalent geometry : angle 0.99791 / 0.60 (46258) hydrogen bonds : bond 0.14179 / 9.78 ( 1458) hydrogen bonds : angle 10.23713 / 7.00 ( 4074) metal coordination : bond 0.16587 / 8.58 ( 6) metal coordination : angle 17.64842 / 11.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 835 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7257 (tt0) cc_final: 0.6986 (mt-10) REVERT: A 95 LYS cc_start: 0.8725 (mttt) cc_final: 0.8514 (mtpt) REVERT: A 97 GLU cc_start: 0.8173 (pt0) cc_final: 0.7556 (pt0) REVERT: A 145 LYS cc_start: 0.6334 (tttt) cc_final: 0.6085 (tttm) REVERT: A 170 ARG cc_start: 0.7140 (mtp180) cc_final: 0.6641 (ptt-90) REVERT: A 181 GLU cc_start: 0.8404 (tp30) cc_final: 0.7779 (mm-30) REVERT: A 192 VAL cc_start: 0.6588 (m) cc_final: 0.6342 (m) REVERT: A 204 GLU cc_start: 0.6925 (tt0) cc_final: 0.6656 (mt-10) REVERT: B 18 GLN cc_start: 0.7967 (pt0) cc_final: 0.7670 (pt0) REVERT: B 95 LYS cc_start: 0.7493 (mmmt) cc_final: 0.6995 (mptt) REVERT: B 171 LEU cc_start: 0.7778 (mt) cc_final: 0.7534 (mm) REVERT: B 194 GLN cc_start: 0.7484 (mm-40) cc_final: 0.7180 (tt0) REVERT: B 197 ASP cc_start: 0.7854 (p0) cc_final: 0.7647 (p0) REVERT: B 200 LYS cc_start: 0.7386 (tttt) cc_final: 0.7049 (tttp) REVERT: B 226 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7350 (mm-30) REVERT: C 20 GLN cc_start: 0.7797 (pp30) cc_final: 0.7178 (pp30) REVERT: C 23 ASP cc_start: 0.8403 (p0) cc_final: 0.8187 (p0) REVERT: C 42 ASP cc_start: 0.7370 (t70) cc_final: 0.7151 (t0) REVERT: C 202 ARG cc_start: 0.6607 (mtp-110) cc_final: 0.6358 (mtp85) REVERT: C 203 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7760 (mtpp) REVERT: C 300 ASP cc_start: 0.5616 (m-30) cc_final: 0.4921 (p0) REVERT: C 314 ASN cc_start: 0.5031 (t0) cc_final: 0.4557 (t0) REVERT: C 337 PHE cc_start: 0.7876 (t80) cc_final: 0.7158 (t80) REVERT: C 394 ARG cc_start: 0.7976 (mtt180) cc_final: 0.7771 (mtp85) REVERT: C 427 ASP cc_start: 0.8189 (m-30) cc_final: 0.7980 (t0) REVERT: C 473 ARG cc_start: 0.7870 (ttt-90) cc_final: 0.7519 (ttp-170) REVERT: C 508 SER cc_start: 0.7626 (m) cc_final: 0.7053 (p) REVERT: C 510 GLN cc_start: 0.8559 (mt0) cc_final: 0.8217 (mm-40) REVERT: C 613 ASN cc_start: 0.8409 (m-40) cc_final: 0.7846 (t0) REVERT: C 624 ASP cc_start: 0.7600 (t0) cc_final: 0.7396 (t70) REVERT: C 645 PHE cc_start: 0.8060 (m-10) cc_final: 0.7677 (m-10) REVERT: C 681 MET cc_start: 0.7253 (mtp) cc_final: 0.6811 (mtt) REVERT: C 696 ASP cc_start: 0.8220 (t70) cc_final: 0.7816 (t0) REVERT: C 768 MET cc_start: 0.7437 (mtp) cc_final: 0.7226 (ptm) REVERT: C 778 GLU cc_start: 0.8057 (tp30) cc_final: 0.7427 (tt0) REVERT: C 779 ARG cc_start: 0.8088 (ttt-90) cc_final: 0.7674 (ttt90) REVERT: C 876 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7854 (mt-10) REVERT: C 890 LYS cc_start: 0.6763 (tptp) cc_final: 0.6124 (pptt) REVERT: C 898 GLU cc_start: 0.8246 (tp30) cc_final: 0.8000 (tp30) REVERT: C 916 SER cc_start: 0.8200 (m) cc_final: 0.7862 (t) REVERT: C 940 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7636 (tm-30) REVERT: C 958 LYS cc_start: 0.7800 (tttm) cc_final: 0.7496 (ttpt) REVERT: C 1028 LYS cc_start: 0.7630 (mtpt) cc_final: 0.7168 (tptp) REVERT: C 1122 LYS cc_start: 0.7866 (ttmp) cc_final: 0.7630 (tttt) REVERT: C 1135 GLN cc_start: 0.7449 (pt0) cc_final: 0.6809 (pp30) REVERT: C 1160 ASP cc_start: 0.7223 (p0) cc_final: 0.6882 (p0) REVERT: C 1170 MET cc_start: 0.7576 (mmp) cc_final: 0.7324 (mmm) REVERT: C 1211 ARG cc_start: 0.7892 (ptp-170) cc_final: 0.7513 (mtm180) REVERT: C 1219 GLU cc_start: 0.8352 (pp20) cc_final: 0.7583 (pt0) REVERT: C 1315 MET cc_start: 0.8888 (ptm) cc_final: 0.8628 (ptm) REVERT: D 42 GLU cc_start: 0.7646 (tt0) cc_final: 0.7349 (tt0) REVERT: D 46 TYR cc_start: 0.5034 (t80) cc_final: 0.4414 (t80) REVERT: D 129 ASP cc_start: 0.7406 (t70) cc_final: 0.7152 (t0) REVERT: D 142 GLU cc_start: 0.8019 (pt0) cc_final: 0.7684 (mm-30) REVERT: D 172 PHE cc_start: 0.6875 (m-80) cc_final: 0.6624 (m-10) REVERT: D 195 GLU cc_start: 0.6011 (tp30) cc_final: 0.5480 (tm-30) REVERT: D 202 ARG cc_start: 0.6171 (mtt-85) cc_final: 0.5198 (tpp-160) REVERT: D 214 ARG cc_start: 0.6714 (ttm-80) cc_final: 0.6360 (ttm170) REVERT: D 222 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7514 (mttp) REVERT: D 225 GLU cc_start: 0.8057 (pt0) cc_final: 0.7515 (tt0) REVERT: D 301 GLU cc_start: 0.7635 (tp30) cc_final: 0.7365 (tm-30) REVERT: D 375 GLU cc_start: 0.7939 (tp30) cc_final: 0.7614 (tp30) REVERT: D 788 LEU cc_start: 0.6966 (tt) cc_final: 0.6308 (mp) REVERT: D 806 ASP cc_start: 0.8794 (m-30) cc_final: 0.8429 (t70) REVERT: D 820 ILE cc_start: 0.6410 (mm) cc_final: 0.6154 (mt) REVERT: D 836 ARG cc_start: 0.8126 (ppp80) cc_final: 0.7822 (tmm-80) REVERT: D 901 ARG cc_start: 0.7973 (mtp180) cc_final: 0.7252 (mtp-110) REVERT: D 907 HIS cc_start: 0.7785 (p90) cc_final: 0.6311 (t70) REVERT: D 985 ILE cc_start: 0.5491 (mm) cc_final: 0.4934 (pt) REVERT: D 992 LYS cc_start: 0.6404 (mtpt) cc_final: 0.6185 (tptp) REVERT: D 1143 ASP cc_start: 0.8151 (t70) cc_final: 0.7912 (t70) REVERT: D 1210 ILE cc_start: 0.7220 (mm) cc_final: 0.6976 (mt) REVERT: D 1231 ARG cc_start: 0.6528 (ttp80) cc_final: 0.6304 (ttm110) REVERT: D 1236 GLU cc_start: 0.8117 (tp30) cc_final: 0.7884 (tp30) REVERT: D 1281 GLU cc_start: 0.6089 (pm20) cc_final: 0.4941 (mt-10) REVERT: D 1284 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7381 (tpt-90) REVERT: D 1307 LEU cc_start: 0.8805 (mp) cc_final: 0.8476 (mt) REVERT: D 1345 ARG cc_start: 0.7998 (ttm170) cc_final: 0.7592 (ttm110) REVERT: F 100 MET cc_start: 0.7388 (ptp) cc_final: 0.6885 (ptp) REVERT: F 260 ARG cc_start: 0.6723 (mtm180) cc_final: 0.6121 (mtp85) REVERT: F 378 GLU cc_start: 0.8648 (tt0) cc_final: 0.8447 (tp30) REVERT: F 405 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7418 (mt) REVERT: F 409 ASN cc_start: 0.8818 (m-40) cc_final: 0.8335 (m-40) REVERT: F 470 MET cc_start: 0.7566 (mmm) cc_final: 0.6991 (mmt) REVERT: F 496 LYS cc_start: 0.7688 (mtmt) cc_final: 0.7371 (tptt) REVERT: F 508 GLU cc_start: 0.7636 (pp20) cc_final: 0.7376 (tm-30) REVERT: F 524 GLU cc_start: 0.8449 (pm20) cc_final: 0.8243 (pm20) REVERT: F 525 ASP cc_start: 0.8781 (t0) cc_final: 0.8393 (t0) REVERT: I 6 ASP cc_start: 0.7550 (m-30) cc_final: 0.7264 (m-30) REVERT: I 24 GLU cc_start: 0.8728 (tp30) cc_final: 0.8372 (tp30) REVERT: I 39 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8139 (mt-10) REVERT: M 98 ARG cc_start: 0.3758 (pmt170) cc_final: 0.3178 (mtt180) REVERT: M 110 MET cc_start: 0.1906 (ttt) cc_final: 0.0876 (ttp) REVERT: M 117 MET cc_start: 0.2858 (ttp) cc_final: 0.2302 (mmt) REVERT: M 141 ILE cc_start: 0.5888 (mt) cc_final: 0.5664 (tt) REVERT: M 153 GLU cc_start: 0.6819 (pt0) cc_final: 0.6575 (pp20) REVERT: M 199 GLU cc_start: 0.5186 (mp0) cc_final: 0.4300 (tp30) outliers start: 23 outliers final: 6 residues processed: 849 average time/residue: 0.2583 time to fit residues: 338.4301 Evaluate side-chains 476 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 469 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain F residue 405 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN B 66 HIS B 147 GLN C 69 GLN C 150 HIS C 343 HIS C 406 ASN C 447 HIS C 551 HIS ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1264 GLN C1268 GLN C1313 HIS D 157 GLN D 320 ASN D 489 ASN D 739 GLN D 792 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1195 GLN D1197 ASN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN F 147 GLN F 301 ASN F 600 HIS M 52 ASN M 124 ASN ** M 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.180606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140658 restraints weight = 50667.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.138637 restraints weight = 87970.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.141299 restraints weight = 71977.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.141398 restraints weight = 44297.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.142649 restraints weight = 39166.595| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 33953 Z= 0.177 Angle : 0.727 9.082 46264 Z= 0.386 Chirality : 0.048 0.242 5282 Planarity : 0.006 0.071 5664 Dihedral : 18.070 144.102 5506 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.51 % Favored : 94.44 % Rotamer: Outliers : 2.81 % Allowed : 9.84 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.12), residues: 3920 helix: -1.50 (0.11), residues: 1584 sheet: -2.02 (0.25), residues: 384 loop : -2.70 (0.12), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1290 TYR 0.030 0.002 TYR M 138 PHE 0.015 0.002 PHE C 385 TRP 0.013 0.002 TRP C 183 HIS 0.012 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (33947) covalent geometry : angle 0.72314 / 0.39 (46258) hydrogen bonds : bond 0.05704 / 3.77 ( 1458) hydrogen bonds : angle 6.61092 / 4.50 ( 4074) metal coordination : bond 0.01279 / 0.67 ( 6) metal coordination : angle 6.59710 / 3.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 514 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 GLN cc_start: 0.7745 (pt0) cc_final: 0.7527 (tt0) REVERT: B 120 ASP cc_start: 0.3181 (p0) cc_final: 0.2419 (p0) REVERT: B 145 LYS cc_start: 0.7990 (tttt) cc_final: 0.7787 (ttmt) REVERT: B 147 GLN cc_start: 0.6977 (mt0) cc_final: 0.6646 (mt0) REVERT: B 200 LYS cc_start: 0.8901 (tttt) cc_final: 0.8668 (tttp) REVERT: C 203 LYS cc_start: 0.8696 (ttmt) cc_final: 0.8305 (mtpp) REVERT: C 434 ASP cc_start: 0.6621 (m-30) cc_final: 0.6160 (m-30) REVERT: C 491 ASP cc_start: 0.8259 (m-30) cc_final: 0.7999 (m-30) REVERT: C 508 SER cc_start: 0.7942 (m) cc_final: 0.7423 (p) REVERT: C 515 MET cc_start: 0.7865 (ttp) cc_final: 0.7646 (ttp) REVERT: C 711 ASP cc_start: 0.7464 (m-30) cc_final: 0.7049 (m-30) REVERT: C 888 THR cc_start: 0.8543 (t) cc_final: 0.7919 (p) REVERT: C 958 LYS cc_start: 0.8917 (tttm) cc_final: 0.8667 (ttmt) REVERT: C 1088 ASP cc_start: 0.8191 (p0) cc_final: 0.7869 (p0) REVERT: C 1122 LYS cc_start: 0.8506 (ttmp) cc_final: 0.8286 (tttt) REVERT: C 1170 MET cc_start: 0.7615 (mmp) cc_final: 0.7345 (mmm) REVERT: C 1219 GLU cc_start: 0.7376 (pp20) cc_final: 0.6707 (pt0) REVERT: C 1315 MET cc_start: 0.8720 (ptm) cc_final: 0.8498 (ptm) REVERT: D 137 ARG cc_start: 0.7788 (mtp85) cc_final: 0.7558 (mtp85) REVERT: D 155 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6111 (tm-30) REVERT: D 298 MET cc_start: 0.5148 (tmt) cc_final: 0.4925 (tmt) REVERT: D 399 LYS cc_start: 0.8426 (mtmm) cc_final: 0.7749 (mmtp) REVERT: D 581 MET cc_start: 0.8609 (mtm) cc_final: 0.8375 (mtp) REVERT: D 833 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7289 (mt-10) REVERT: D 901 ARG cc_start: 0.8206 (mtp180) cc_final: 0.7970 (mtp-110) REVERT: D 907 HIS cc_start: 0.7015 (p90) cc_final: 0.6611 (t70) REVERT: D 985 ILE cc_start: 0.6989 (mm) cc_final: 0.6154 (pt) REVERT: D 1143 ASP cc_start: 0.7905 (t70) cc_final: 0.7626 (t70) REVERT: D 1195 GLN cc_start: 0.6667 (OUTLIER) cc_final: 0.6369 (tt0) REVERT: D 1282 TYR cc_start: 0.8049 (t80) cc_final: 0.7419 (t80) REVERT: E 30 MET cc_start: 0.7976 (mtp) cc_final: 0.7058 (ttm) REVERT: F 102 MET cc_start: 0.7963 (mmt) cc_final: 0.7719 (mmt) REVERT: F 260 ARG cc_start: 0.5266 (mtm180) cc_final: 0.4825 (mtp85) REVERT: F 264 LYS cc_start: 0.5496 (mptt) cc_final: 0.5238 (tptp) REVERT: F 405 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8848 (mm) REVERT: F 508 GLU cc_start: 0.7454 (pp20) cc_final: 0.7225 (tm-30) REVERT: I 10 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: I 64 GLU cc_start: 0.6879 (pp20) cc_final: 0.6617 (pp20) REVERT: M 98 ARG cc_start: 0.4708 (pmt170) cc_final: 0.3319 (mtt180) REVERT: M 196 ARG cc_start: 0.3071 (ptt180) cc_final: 0.0961 (mtp85) REVERT: M 199 GLU cc_start: 0.4942 (mp0) cc_final: 0.4243 (tp30) outliers start: 95 outliers final: 54 residues processed: 582 average time/residue: 0.2424 time to fit residues: 223.3570 Evaluate side-chains 443 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 385 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 983 LYS Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1195 GLN Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 502 LYS Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain M residue 40 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 53 optimal weight: 5.9990 chunk 247 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 241 optimal weight: 0.2980 chunk 14 optimal weight: 10.0000 chunk 380 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 371 optimal weight: 7.9990 chunk 337 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 186 optimal weight: 0.0010 overall best weight: 2.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 HIS B 103 ASN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 761 GLN ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN M 90 ASN ** M 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.177038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138755 restraints weight = 50309.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.138821 restraints weight = 108540.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141269 restraints weight = 71287.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.141258 restraints weight = 44881.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.142627 restraints weight = 37298.808| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33953 Z= 0.188 Angle : 0.698 8.940 46264 Z= 0.371 Chirality : 0.047 0.278 5282 Planarity : 0.005 0.073 5664 Dihedral : 17.889 143.111 5503 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.84 % Favored : 94.13 % Rotamer: Outliers : 3.10 % Allowed : 12.73 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.58 (0.12), residues: 3920 helix: -0.76 (0.12), residues: 1588 sheet: -1.85 (0.25), residues: 371 loop : -2.54 (0.12), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1242 TYR 0.018 0.002 TYR D 165 PHE 0.016 0.002 PHE D 172 TRP 0.010 0.002 TRP C 183 HIS 0.006 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (33947) covalent geometry : angle 0.69535 / 0.37 (46258) hydrogen bonds : bond 0.05362 / 3.52 ( 1458) hydrogen bonds : angle 5.83395 / 3.99 ( 4074) metal coordination : bond 0.00518 / 0.29 ( 6) metal coordination : angle 5.44653 / 3.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 421 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 VAL cc_start: 0.9411 (OUTLIER) cc_final: 0.9185 (m) REVERT: A 80 GLU cc_start: 0.7680 (pp20) cc_final: 0.7398 (tm-30) REVERT: A 145 LYS cc_start: 0.8929 (tttt) cc_final: 0.8555 (tttt) REVERT: B 93 GLN cc_start: 0.6527 (tp40) cc_final: 0.5837 (mp10) REVERT: B 200 LYS cc_start: 0.8945 (tttt) cc_final: 0.8694 (tttp) REVERT: C 163 LYS cc_start: 0.3734 (OUTLIER) cc_final: 0.3454 (pttp) REVERT: C 203 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8168 (mtpp) REVERT: C 314 ASN cc_start: 0.6301 (t0) cc_final: 0.6014 (t0) REVERT: C 343 HIS cc_start: 0.6626 (m90) cc_final: 0.6072 (m90) REVERT: C 352 ARG cc_start: 0.7857 (mtp180) cc_final: 0.7496 (mmm-85) REVERT: C 434 ASP cc_start: 0.6496 (m-30) cc_final: 0.5981 (m-30) REVERT: C 491 ASP cc_start: 0.8085 (m-30) cc_final: 0.7839 (m-30) REVERT: C 508 SER cc_start: 0.7735 (m) cc_final: 0.7271 (p) REVERT: C 711 ASP cc_start: 0.7512 (m-30) cc_final: 0.7104 (m-30) REVERT: C 888 THR cc_start: 0.8583 (t) cc_final: 0.8118 (p) REVERT: C 947 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7638 (tm-30) REVERT: C 958 LYS cc_start: 0.8881 (tttm) cc_final: 0.8566 (ttpt) REVERT: C 1088 ASP cc_start: 0.8283 (p0) cc_final: 0.8050 (p0) REVERT: C 1122 LYS cc_start: 0.8651 (ttmp) cc_final: 0.8444 (tttt) REVERT: C 1219 GLU cc_start: 0.7613 (pp20) cc_final: 0.6844 (pt0) REVERT: C 1315 MET cc_start: 0.8829 (ptm) cc_final: 0.8580 (ptm) REVERT: D 34 SER cc_start: 0.9306 (t) cc_final: 0.8716 (p) REVERT: D 155 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.5914 (tm-30) REVERT: D 279 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9108 (tt) REVERT: D 298 MET cc_start: 0.6060 (tmt) cc_final: 0.5316 (tmt) REVERT: D 399 LYS cc_start: 0.8470 (mtmm) cc_final: 0.7712 (mmtp) REVERT: D 466 MET cc_start: 0.8238 (mtp) cc_final: 0.8002 (ttm) REVERT: D 581 MET cc_start: 0.8751 (mtm) cc_final: 0.8434 (mtp) REVERT: D 625 MET cc_start: 0.8570 (ttp) cc_final: 0.8322 (ttp) REVERT: D 902 ASP cc_start: 0.8321 (t70) cc_final: 0.7895 (t0) REVERT: D 907 HIS cc_start: 0.7176 (p90) cc_final: 0.6875 (t70) REVERT: D 1195 GLN cc_start: 0.6954 (pp30) cc_final: 0.6378 (tt0) REVERT: E 30 MET cc_start: 0.7920 (mtp) cc_final: 0.7018 (ttm) REVERT: F 105 MET cc_start: 0.8462 (ppp) cc_final: 0.8091 (ppp) REVERT: F 260 ARG cc_start: 0.4906 (mtm180) cc_final: 0.4435 (mtp85) REVERT: F 264 LYS cc_start: 0.5943 (mptt) cc_final: 0.5418 (tptp) REVERT: F 293 GLU cc_start: 0.4983 (mp0) cc_final: 0.4665 (mp0) REVERT: F 379 MET cc_start: 0.8785 (tpp) cc_final: 0.8554 (tpp) REVERT: F 450 ILE cc_start: 0.8487 (mp) cc_final: 0.8127 (mt) REVERT: I 64 GLU cc_start: 0.6948 (pp20) cc_final: 0.6574 (pp20) REVERT: M 98 ARG cc_start: 0.4499 (pmt170) cc_final: 0.3126 (mtt180) REVERT: M 199 GLU cc_start: 0.5104 (mp0) cc_final: 0.4693 (tp30) outliers start: 105 outliers final: 62 residues processed: 505 average time/residue: 0.2239 time to fit residues: 185.6177 Evaluate side-chains 419 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 353 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 983 LYS Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1257 VAL Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain M residue 190 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 281 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 379 optimal weight: 30.0000 chunk 344 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 327 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 339 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 GLN B 103 ASN B 147 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 808 ASN C1136 GLN ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN C1264 GLN D 739 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 ASN M 156 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.172269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.133164 restraints weight = 49751.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.126099 restraints weight = 83640.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.122458 restraints weight = 63604.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122244 restraints weight = 63089.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.122782 restraints weight = 48053.494| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 33953 Z= 0.266 Angle : 0.757 8.726 46264 Z= 0.399 Chirality : 0.049 0.236 5282 Planarity : 0.006 0.065 5664 Dihedral : 17.826 143.703 5501 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.73 % Favored : 93.24 % Rotamer: Outliers : 3.87 % Allowed : 14.12 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.40 (0.12), residues: 3920 helix: -0.47 (0.13), residues: 1582 sheet: -1.93 (0.24), residues: 424 loop : -2.53 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 425 TYR 0.018 0.002 TYR D1363 PHE 0.024 0.002 PHE D 620 TRP 0.012 0.002 TRP F 326 HIS 0.010 0.002 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.27 (33947) covalent geometry : angle 0.75344 / 0.40 (46258) hydrogen bonds : bond 0.05715 / 3.78 ( 1458) hydrogen bonds : angle 5.53705 / 3.78 ( 4074) metal coordination : bond 0.01048 / 0.61 ( 6) metal coordination : angle 6.06999 / 3.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 384 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.6987 (t0) REVERT: A 102 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9141 (tp) REVERT: C 163 LYS cc_start: 0.3968 (OUTLIER) cc_final: 0.3394 (pttp) REVERT: C 199 ASP cc_start: 0.7410 (m-30) cc_final: 0.7164 (t0) REVERT: C 203 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8301 (mtpp) REVERT: C 314 ASN cc_start: 0.6215 (t0) cc_final: 0.5975 (t0) REVERT: C 343 HIS cc_start: 0.6626 (m90) cc_final: 0.6118 (m90) REVERT: C 434 ASP cc_start: 0.6647 (m-30) cc_final: 0.6087 (m-30) REVERT: C 508 SER cc_start: 0.7970 (m) cc_final: 0.7478 (p) REVERT: C 645 PHE cc_start: 0.8581 (m-10) cc_final: 0.8359 (m-10) REVERT: C 711 ASP cc_start: 0.7593 (m-30) cc_final: 0.7230 (m-30) REVERT: C 958 LYS cc_start: 0.8917 (tttm) cc_final: 0.8564 (ttpt) REVERT: C 1122 LYS cc_start: 0.8769 (ttmp) cc_final: 0.8486 (tttt) REVERT: C 1219 GLU cc_start: 0.7943 (pp20) cc_final: 0.7221 (pt0) REVERT: C 1319 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7521 (tpp) REVERT: D 34 SER cc_start: 0.9449 (t) cc_final: 0.8812 (p) REVERT: D 155 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6393 (tm-30) REVERT: D 233 LYS cc_start: 0.8161 (mttm) cc_final: 0.7903 (mmtt) REVERT: D 295 GLU cc_start: 0.7768 (tp30) cc_final: 0.7125 (tp30) REVERT: D 298 MET cc_start: 0.5783 (tmt) cc_final: 0.5172 (tmt) REVERT: D 399 LYS cc_start: 0.8471 (mtmm) cc_final: 0.8129 (mtmm) REVERT: D 429 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8642 (mt) REVERT: D 581 MET cc_start: 0.8811 (mtm) cc_final: 0.8366 (mtp) REVERT: D 747 MET cc_start: 0.6747 (pmm) cc_final: 0.6505 (pmm) REVERT: D 788 LEU cc_start: 0.8069 (tt) cc_final: 0.7523 (mp) REVERT: D 1025 MET cc_start: 0.6896 (tpt) cc_final: 0.6234 (mtp) REVERT: D 1195 GLN cc_start: 0.6995 (pp30) cc_final: 0.6781 (pp30) REVERT: E 30 MET cc_start: 0.8016 (mtp) cc_final: 0.6938 (ttm) REVERT: F 102 MET cc_start: 0.8056 (mmt) cc_final: 0.7834 (mmt) REVERT: F 260 ARG cc_start: 0.5495 (mtm180) cc_final: 0.4826 (mtp85) REVERT: F 264 LYS cc_start: 0.6004 (mptt) cc_final: 0.5608 (tptp) REVERT: F 409 ASN cc_start: 0.9035 (m-40) cc_final: 0.8707 (m-40) REVERT: F 456 MET cc_start: 0.7498 (mtm) cc_final: 0.7248 (ttm) REVERT: F 474 MET cc_start: 0.8006 (ppp) cc_final: 0.7571 (ppp) REVERT: I 6 ASP cc_start: 0.7880 (p0) cc_final: 0.7634 (p0) REVERT: I 10 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: I 64 GLU cc_start: 0.7509 (pp20) cc_final: 0.7202 (pp20) REVERT: M 98 ARG cc_start: 0.4237 (pmt170) cc_final: 0.3038 (mtt180) REVERT: M 199 GLU cc_start: 0.5303 (mp0) cc_final: 0.4780 (tp30) outliers start: 131 outliers final: 81 residues processed: 488 average time/residue: 0.2228 time to fit residues: 176.9059 Evaluate side-chains 425 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 337 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 923 ILE Chi-restraints excluded: chain D residue 983 LYS Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1257 VAL Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 389 SER Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 190 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 183 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 15 optimal weight: 0.0030 chunk 58 optimal weight: 0.9980 chunk 304 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 340 optimal weight: 6.9990 chunk 173 optimal weight: 0.8980 chunk 225 optimal weight: 0.9980 chunk 242 optimal weight: 10.0000 chunk 260 optimal weight: 4.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 147 GLN C 69 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 739 GLN D 805 GLN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.178449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138150 restraints weight = 50255.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.133912 restraints weight = 73616.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.128735 restraints weight = 53285.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128018 restraints weight = 61965.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128771 restraints weight = 51847.136| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33953 Z= 0.125 Angle : 0.616 9.018 46264 Z= 0.328 Chirality : 0.044 0.209 5282 Planarity : 0.004 0.058 5664 Dihedral : 17.640 142.431 5501 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.20 % Rotamer: Outliers : 2.63 % Allowed : 15.95 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.13), residues: 3920 helix: -0.03 (0.13), residues: 1595 sheet: -1.68 (0.24), residues: 417 loop : -2.34 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1034 TYR 0.018 0.001 TYR A 185 PHE 0.017 0.001 PHE C 337 TRP 0.012 0.001 TRP F 326 HIS 0.006 0.001 HIS M 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (33947) covalent geometry : angle 0.61383 / 0.33 (46258) hydrogen bonds : bond 0.04728 / 3.09 ( 1458) hydrogen bonds : angle 5.07464 / 3.46 ( 4074) metal coordination : bond 0.00203 / 0.10 ( 6) metal coordination : angle 4.19950 / 2.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 391 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.7316 (t70) cc_final: 0.6960 (t0) REVERT: A 102 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9062 (tp) REVERT: A 200 LYS cc_start: 0.9102 (ptmt) cc_final: 0.8735 (ptmm) REVERT: B 93 GLN cc_start: 0.6467 (tp40) cc_final: 0.5491 (mp10) REVERT: B 127 GLN cc_start: 0.8118 (mp10) cc_final: 0.7748 (pt0) REVERT: C 36 GLN cc_start: 0.7730 (tp40) cc_final: 0.7461 (tp-100) REVERT: C 163 LYS cc_start: 0.3722 (OUTLIER) cc_final: 0.3172 (pttp) REVERT: C 199 ASP cc_start: 0.7434 (m-30) cc_final: 0.6961 (t0) REVERT: C 203 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8148 (mtpp) REVERT: C 314 ASN cc_start: 0.6153 (t0) cc_final: 0.5923 (t0) REVERT: C 369 MET cc_start: 0.7611 (tmm) cc_final: 0.7266 (ttt) REVERT: C 434 ASP cc_start: 0.6560 (m-30) cc_final: 0.6094 (m-30) REVERT: C 508 SER cc_start: 0.7618 (m) cc_final: 0.7096 (p) REVERT: C 711 ASP cc_start: 0.7559 (m-30) cc_final: 0.7246 (m-30) REVERT: C 958 LYS cc_start: 0.8856 (tttm) cc_final: 0.8473 (ttpt) REVERT: C 1122 LYS cc_start: 0.8578 (ttmp) cc_final: 0.8339 (tttt) REVERT: C 1219 GLU cc_start: 0.7270 (pp20) cc_final: 0.6947 (pt0) REVERT: D 34 SER cc_start: 0.9496 (t) cc_final: 0.8766 (p) REVERT: D 218 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8457 (t) REVERT: D 298 MET cc_start: 0.6121 (tmt) cc_final: 0.5280 (tmt) REVERT: D 484 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8225 (mtm) REVERT: D 581 MET cc_start: 0.8685 (mtm) cc_final: 0.8388 (mtp) REVERT: D 747 MET cc_start: 0.6523 (pmm) cc_final: 0.6248 (pmm) REVERT: D 825 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8234 (p) REVERT: D 832 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8002 (mtmm) REVERT: D 902 ASP cc_start: 0.8367 (t70) cc_final: 0.8104 (t0) REVERT: D 1025 MET cc_start: 0.6721 (tpt) cc_final: 0.5855 (mtp) REVERT: D 1266 ILE cc_start: 0.7123 (tp) cc_final: 0.6836 (mt) REVERT: E 30 MET cc_start: 0.7814 (mtp) cc_final: 0.6711 (ttm) REVERT: F 260 ARG cc_start: 0.5300 (mtm180) cc_final: 0.4664 (mtp85) REVERT: F 264 LYS cc_start: 0.6114 (mptt) cc_final: 0.5785 (tptp) REVERT: F 293 GLU cc_start: 0.5293 (mp0) cc_final: 0.4794 (mp0) REVERT: F 335 GLU cc_start: 0.4044 (tm-30) cc_final: 0.3592 (mp0) REVERT: F 409 ASN cc_start: 0.8892 (m-40) cc_final: 0.8568 (m-40) REVERT: F 474 MET cc_start: 0.8057 (ppp) cc_final: 0.6948 (tmm) REVERT: I 10 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: I 64 GLU cc_start: 0.7571 (pp20) cc_final: 0.6930 (pp20) REVERT: M 98 ARG cc_start: 0.4226 (pmt170) cc_final: 0.2855 (mtt180) REVERT: M 199 GLU cc_start: 0.5200 (mp0) cc_final: 0.4613 (tp30) outliers start: 89 outliers final: 53 residues processed: 454 average time/residue: 0.2095 time to fit residues: 156.1474 Evaluate side-chains 402 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 342 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 186 LYS Chi-restraints excluded: chain M residue 190 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 288 optimal weight: 5.9990 chunk 161 optimal weight: 0.0970 chunk 5 optimal weight: 0.5980 chunk 368 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 309 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 330 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 262 optimal weight: 10.0000 overall best weight: 2.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 147 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.176934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3519 r_free = 0.3519 target = 0.130201 restraints weight = 50178.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123405 restraints weight = 54094.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124114 restraints weight = 56137.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124521 restraints weight = 48718.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124721 restraints weight = 44495.755| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33953 Z= 0.153 Angle : 0.623 11.124 46264 Z= 0.330 Chirality : 0.045 0.237 5282 Planarity : 0.004 0.054 5664 Dihedral : 17.542 141.577 5501 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.64 % Favored : 94.34 % Rotamer: Outliers : 2.84 % Allowed : 16.48 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.13), residues: 3920 helix: 0.19 (0.13), residues: 1589 sheet: -1.55 (0.24), residues: 417 loop : -2.26 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1231 TYR 0.018 0.001 TYR F 571 PHE 0.015 0.001 PHE C1221 TRP 0.011 0.001 TRP F 326 HIS 0.007 0.001 HIS M 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (33947) covalent geometry : angle 0.62108 / 0.33 (46258) hydrogen bonds : bond 0.04743 / 3.10 ( 1458) hydrogen bonds : angle 4.91525 / 3.35 ( 4074) metal coordination : bond 0.00418 / 0.23 ( 6) metal coordination : angle 4.15302 / 2.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 367 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.7366 (t70) cc_final: 0.7021 (t0) REVERT: A 102 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9125 (tp) REVERT: A 145 LYS cc_start: 0.8846 (tttt) cc_final: 0.8397 (tttm) REVERT: B 93 GLN cc_start: 0.6525 (tp40) cc_final: 0.5477 (mp10) REVERT: B 127 GLN cc_start: 0.8144 (mp10) cc_final: 0.7788 (pt0) REVERT: C 36 GLN cc_start: 0.7815 (tp40) cc_final: 0.7427 (tp-100) REVERT: C 163 LYS cc_start: 0.4053 (OUTLIER) cc_final: 0.3390 (pttp) REVERT: C 199 ASP cc_start: 0.7694 (m-30) cc_final: 0.7098 (t0) REVERT: C 203 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8297 (mtpp) REVERT: C 314 ASN cc_start: 0.6102 (t0) cc_final: 0.5895 (t0) REVERT: C 434 ASP cc_start: 0.6597 (m-30) cc_final: 0.6029 (m-30) REVERT: C 508 SER cc_start: 0.7820 (m) cc_final: 0.7275 (p) REVERT: C 711 ASP cc_start: 0.7638 (m-30) cc_final: 0.7330 (m-30) REVERT: C 958 LYS cc_start: 0.8849 (tttm) cc_final: 0.8466 (ttpt) REVERT: C 1219 GLU cc_start: 0.7867 (pp20) cc_final: 0.7364 (pt0) REVERT: D 34 SER cc_start: 0.9604 (t) cc_final: 0.8900 (p) REVERT: D 45 ASN cc_start: 0.7994 (t0) cc_final: 0.7786 (t0) REVERT: D 155 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6485 (tm-30) REVERT: D 225 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6563 (tp30) REVERT: D 298 MET cc_start: 0.6160 (tmt) cc_final: 0.5293 (tmt) REVERT: D 484 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8385 (mtm) REVERT: D 581 MET cc_start: 0.8761 (mtm) cc_final: 0.8282 (mtp) REVERT: D 747 MET cc_start: 0.6552 (pmm) cc_final: 0.6324 (pmm) REVERT: D 832 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7930 (mtmt) REVERT: D 1143 ASP cc_start: 0.8116 (t70) cc_final: 0.7888 (t70) REVERT: D 1144 LEU cc_start: 0.8970 (tp) cc_final: 0.8762 (tp) REVERT: D 1266 ILE cc_start: 0.7185 (tp) cc_final: 0.6909 (mt) REVERT: E 12 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7689 (ttmm) REVERT: E 30 MET cc_start: 0.7586 (mtp) cc_final: 0.6763 (ttm) REVERT: F 102 MET cc_start: 0.8222 (mmt) cc_final: 0.7937 (mmt) REVERT: F 260 ARG cc_start: 0.5691 (mtm180) cc_final: 0.4880 (mtp85) REVERT: F 264 LYS cc_start: 0.6093 (mptt) cc_final: 0.5765 (tptp) REVERT: F 335 GLU cc_start: 0.4089 (tm-30) cc_final: 0.3634 (mp0) REVERT: F 374 ARG cc_start: 0.7715 (ppp-140) cc_final: 0.7308 (tpp80) REVERT: F 409 ASN cc_start: 0.8946 (m-40) cc_final: 0.8554 (m-40) REVERT: F 474 MET cc_start: 0.7980 (ppp) cc_final: 0.7741 (ppp) REVERT: I 10 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: I 43 THR cc_start: 0.7835 (m) cc_final: 0.7625 (p) REVERT: I 64 GLU cc_start: 0.7656 (pp20) cc_final: 0.7033 (pp20) REVERT: I 78 GLU cc_start: 0.7674 (tp30) cc_final: 0.7464 (mm-30) REVERT: M 98 ARG cc_start: 0.4487 (pmt170) cc_final: 0.2895 (mtt180) REVERT: M 199 GLU cc_start: 0.5363 (mp0) cc_final: 0.4386 (tp30) outliers start: 96 outliers final: 66 residues processed: 440 average time/residue: 0.2151 time to fit residues: 155.0178 Evaluate side-chains 419 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 345 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 983 LYS Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 190 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 214 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 366 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 chunk 389 optimal weight: 7.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 ASN ** M 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.175681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.138106 restraints weight = 50119.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.139785 restraints weight = 124946.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.141192 restraints weight = 65553.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.142813 restraints weight = 40048.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.143026 restraints weight = 32967.889| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33953 Z= 0.161 Angle : 0.620 11.112 46264 Z= 0.329 Chirality : 0.045 0.270 5282 Planarity : 0.004 0.065 5664 Dihedral : 17.470 141.781 5501 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.49 % Rotamer: Outliers : 3.22 % Allowed : 16.57 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.13), residues: 3920 helix: 0.29 (0.13), residues: 1596 sheet: -1.46 (0.24), residues: 418 loop : -2.20 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 53 TYR 0.021 0.001 TYR F 268 PHE 0.018 0.001 PHE C 337 TRP 0.011 0.001 TRP F 326 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (33947) covalent geometry : angle 0.61798 / 0.33 (46258) hydrogen bonds : bond 0.04725 / 3.08 ( 1458) hydrogen bonds : angle 4.80571 / 3.28 ( 4074) metal coordination : bond 0.00520 / 0.29 ( 6) metal coordination : angle 3.98666 / 2.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 363 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7660 (tp30) cc_final: 0.7202 (mt-10) REVERT: A 62 ASP cc_start: 0.7285 (t70) cc_final: 0.6877 (t0) REVERT: A 102 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9108 (tp) REVERT: A 145 LYS cc_start: 0.8819 (tttt) cc_final: 0.8354 (tttm) REVERT: C 36 GLN cc_start: 0.7652 (tp40) cc_final: 0.7332 (tp-100) REVERT: C 163 LYS cc_start: 0.4023 (OUTLIER) cc_final: 0.3327 (pttp) REVERT: C 199 ASP cc_start: 0.7458 (m-30) cc_final: 0.7115 (t0) REVERT: C 203 LYS cc_start: 0.8653 (ttmt) cc_final: 0.8161 (mtpp) REVERT: C 314 ASN cc_start: 0.6314 (t0) cc_final: 0.6025 (t0) REVERT: C 434 ASP cc_start: 0.6352 (m-30) cc_final: 0.5925 (m-30) REVERT: C 496 LYS cc_start: 0.6944 (OUTLIER) cc_final: 0.6717 (pttp) REVERT: C 508 SER cc_start: 0.7676 (m) cc_final: 0.7293 (p) REVERT: C 711 ASP cc_start: 0.7664 (m-30) cc_final: 0.7370 (m-30) REVERT: C 958 LYS cc_start: 0.8816 (tttm) cc_final: 0.8441 (ttpt) REVERT: C 1219 GLU cc_start: 0.7545 (pp20) cc_final: 0.7306 (pt0) REVERT: D 298 MET cc_start: 0.6031 (tmt) cc_final: 0.5234 (tmt) REVERT: D 429 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8654 (mt) REVERT: D 484 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8603 (mtm) REVERT: D 581 MET cc_start: 0.8888 (mtm) cc_final: 0.8356 (mtp) REVERT: D 747 MET cc_start: 0.6408 (pmm) cc_final: 0.6184 (pmm) REVERT: D 825 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8094 (p) REVERT: D 832 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7502 (mtmt) REVERT: D 1143 ASP cc_start: 0.7970 (t70) cc_final: 0.7736 (t70) REVERT: D 1144 LEU cc_start: 0.8965 (tp) cc_final: 0.8748 (tp) REVERT: D 1266 ILE cc_start: 0.6889 (tp) cc_final: 0.6611 (mt) REVERT: D 1287 ILE cc_start: 0.8136 (pp) cc_final: 0.7933 (pt) REVERT: E 12 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7731 (ttmm) REVERT: F 260 ARG cc_start: 0.4938 (mtm180) cc_final: 0.4514 (mtp85) REVERT: F 264 LYS cc_start: 0.6245 (mptt) cc_final: 0.5988 (tptp) REVERT: F 268 TYR cc_start: 0.6096 (t80) cc_final: 0.5828 (t80) REVERT: F 293 GLU cc_start: 0.5622 (mp0) cc_final: 0.4851 (mp0) REVERT: F 409 ASN cc_start: 0.9009 (m-40) cc_final: 0.8529 (m-40) REVERT: F 413 MET cc_start: 0.7858 (mtp) cc_final: 0.7653 (mtm) REVERT: F 474 MET cc_start: 0.7863 (ppp) cc_final: 0.7446 (ppp) REVERT: I 10 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: I 64 GLU cc_start: 0.7366 (pp20) cc_final: 0.6803 (pp20) REVERT: M 98 ARG cc_start: 0.4420 (pmt170) cc_final: 0.2924 (mtt180) REVERT: M 199 GLU cc_start: 0.4711 (mp0) cc_final: 0.4107 (tp30) outliers start: 109 outliers final: 77 residues processed: 444 average time/residue: 0.2166 time to fit residues: 155.8675 Evaluate side-chains 427 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 341 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 983 LYS Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain M residue 12 ASN Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 186 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 394 optimal weight: 50.0000 chunk 314 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 384 optimal weight: 0.0270 chunk 287 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 333 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 290 optimal weight: 9.9990 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN D 777 HIS ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 137 ASN M 157 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.173941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.136727 restraints weight = 49579.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.128577 restraints weight = 83584.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.125501 restraints weight = 70661.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.125535 restraints weight = 67870.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.125850 restraints weight = 52218.668| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33953 Z= 0.192 Angle : 0.648 12.726 46264 Z= 0.342 Chirality : 0.045 0.259 5282 Planarity : 0.004 0.052 5664 Dihedral : 17.435 142.129 5501 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.35 % Favored : 93.62 % Rotamer: Outliers : 3.28 % Allowed : 16.87 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.13), residues: 3920 helix: 0.32 (0.13), residues: 1594 sheet: -1.38 (0.24), residues: 417 loop : -2.20 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 560 TYR 0.019 0.002 TYR M 134 PHE 0.017 0.002 PHE F 316 TRP 0.021 0.002 TRP C 997 HIS 0.006 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (33947) covalent geometry : angle 0.64643 / 0.34 (46258) hydrogen bonds : bond 0.04872 / 3.17 ( 1458) hydrogen bonds : angle 4.78946 / 3.27 ( 4074) metal coordination : bond 0.00672 / 0.39 ( 6) metal coordination : angle 4.15986 / 2.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 358 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.7422 (t70) cc_final: 0.7055 (t0) REVERT: A 102 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9137 (tp) REVERT: A 145 LYS cc_start: 0.8926 (tttt) cc_final: 0.8625 (tttm) REVERT: B 93 GLN cc_start: 0.6753 (tp40) cc_final: 0.5704 (mp10) REVERT: B 127 GLN cc_start: 0.7811 (pm20) cc_final: 0.7305 (pt0) REVERT: C 36 GLN cc_start: 0.7877 (tp40) cc_final: 0.7523 (tp-100) REVERT: C 163 LYS cc_start: 0.4298 (OUTLIER) cc_final: 0.3688 (pptt) REVERT: C 203 LYS cc_start: 0.8862 (ttmt) cc_final: 0.8247 (mtpp) REVERT: C 314 ASN cc_start: 0.6229 (t0) cc_final: 0.5970 (t0) REVERT: C 434 ASP cc_start: 0.6560 (m-30) cc_final: 0.6053 (m-30) REVERT: C 496 LYS cc_start: 0.6792 (OUTLIER) cc_final: 0.6537 (pttp) REVERT: C 508 SER cc_start: 0.7853 (m) cc_final: 0.7431 (p) REVERT: C 711 ASP cc_start: 0.7668 (m-30) cc_final: 0.7414 (m-30) REVERT: C 958 LYS cc_start: 0.8877 (tttm) cc_final: 0.8629 (ttpt) REVERT: C 1025 PHE cc_start: 0.6240 (t80) cc_final: 0.5818 (m-80) REVERT: C 1219 GLU cc_start: 0.7813 (pp20) cc_final: 0.7510 (pt0) REVERT: D 225 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6897 (tp30) REVERT: D 295 GLU cc_start: 0.7788 (tp30) cc_final: 0.7122 (tp30) REVERT: D 298 MET cc_start: 0.6115 (tmt) cc_final: 0.5299 (tmt) REVERT: D 399 LYS cc_start: 0.8384 (mtmm) cc_final: 0.8167 (mtmm) REVERT: D 429 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8652 (mt) REVERT: D 484 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8398 (mtm) REVERT: D 581 MET cc_start: 0.8775 (mtm) cc_final: 0.8310 (mtp) REVERT: D 825 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8169 (p) REVERT: D 832 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7957 (mtmt) REVERT: D 1143 ASP cc_start: 0.8190 (t70) cc_final: 0.7960 (t70) REVERT: D 1144 LEU cc_start: 0.8956 (tp) cc_final: 0.8756 (tp) REVERT: D 1266 ILE cc_start: 0.7241 (tp) cc_final: 0.6996 (mt) REVERT: E 12 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7654 (ttmm) REVERT: F 260 ARG cc_start: 0.5529 (mtm180) cc_final: 0.4792 (mtp85) REVERT: F 264 LYS cc_start: 0.6307 (mptt) cc_final: 0.5976 (tptp) REVERT: F 268 TYR cc_start: 0.6221 (t80) cc_final: 0.6004 (t80) REVERT: F 409 ASN cc_start: 0.9021 (m-40) cc_final: 0.8606 (m-40) REVERT: F 474 MET cc_start: 0.7877 (ppp) cc_final: 0.7284 (ppp) REVERT: I 10 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: I 64 GLU cc_start: 0.7762 (pp20) cc_final: 0.7121 (pp20) REVERT: M 98 ARG cc_start: 0.4356 (pmt170) cc_final: 0.2857 (mtt180) REVERT: M 167 MET cc_start: 0.3013 (mmm) cc_final: 0.2722 (tpp) REVERT: M 199 GLU cc_start: 0.5101 (mp0) cc_final: 0.4292 (tp30) outliers start: 111 outliers final: 84 residues processed: 439 average time/residue: 0.2123 time to fit residues: 152.8595 Evaluate side-chains 434 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 340 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 835 LEU Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 923 ILE Chi-restraints excluded: chain D residue 983 LYS Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 152 PHE Chi-restraints excluded: chain M residue 186 LYS Chi-restraints excluded: chain M residue 190 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 225 optimal weight: 1.9990 chunk 338 optimal weight: 30.0000 chunk 179 optimal weight: 0.0770 chunk 257 optimal weight: 0.8980 chunk 239 optimal weight: 30.0000 chunk 4 optimal weight: 5.9990 chunk 387 optimal weight: 30.0000 chunk 84 optimal weight: 7.9990 chunk 266 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 176 optimal weight: 0.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.177129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 132)---------------| | r_work = 0.3541 r_free = 0.3541 target = 0.131995 restraints weight = 49759.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.125605 restraints weight = 53767.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.125874 restraints weight = 52708.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126708 restraints weight = 46266.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.126794 restraints weight = 42140.966| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33953 Z= 0.120 Angle : 0.601 13.277 46264 Z= 0.317 Chirality : 0.043 0.243 5282 Planarity : 0.004 0.061 5664 Dihedral : 17.296 141.435 5501 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.72 % Favored : 95.26 % Rotamer: Outliers : 2.57 % Allowed : 17.73 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.13), residues: 3920 helix: 0.51 (0.13), residues: 1600 sheet: -1.28 (0.25), residues: 404 loop : -2.08 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C1034 TYR 0.028 0.001 TYR M 134 PHE 0.018 0.001 PHE F 316 TRP 0.012 0.001 TRP C 997 HIS 0.004 0.001 HIS M 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (33947) covalent geometry : angle 0.59966 / 0.32 (46258) hydrogen bonds : bond 0.04410 / 2.85 ( 1458) hydrogen bonds : angle 4.59461 / 3.13 ( 4074) metal coordination : bond 0.00250 / 0.13 ( 6) metal coordination : angle 3.38652 / 2.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 363 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.7309 (t70) cc_final: 0.6936 (t0) REVERT: A 102 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9102 (tp) REVERT: A 145 LYS cc_start: 0.8888 (tttt) cc_final: 0.8413 (tttm) REVERT: B 93 GLN cc_start: 0.6707 (tp40) cc_final: 0.5609 (mp10) REVERT: B 127 GLN cc_start: 0.8013 (pm20) cc_final: 0.7401 (pt0) REVERT: C 36 GLN cc_start: 0.7863 (tp40) cc_final: 0.7502 (tp-100) REVERT: C 163 LYS cc_start: 0.4230 (OUTLIER) cc_final: 0.3751 (pptt) REVERT: C 203 LYS cc_start: 0.8873 (ttmt) cc_final: 0.8568 (ttmm) REVERT: C 314 ASN cc_start: 0.6171 (t0) cc_final: 0.5902 (t0) REVERT: C 434 ASP cc_start: 0.6383 (m-30) cc_final: 0.5768 (m-30) REVERT: C 496 LYS cc_start: 0.6786 (OUTLIER) cc_final: 0.6482 (pttp) REVERT: C 711 ASP cc_start: 0.7640 (m-30) cc_final: 0.7312 (m-30) REVERT: C 958 LYS cc_start: 0.8884 (tttm) cc_final: 0.8444 (ttpt) REVERT: C 1025 PHE cc_start: 0.6247 (t80) cc_final: 0.5893 (m-80) REVERT: C 1119 MET cc_start: 0.9069 (tpt) cc_final: 0.8610 (tpt) REVERT: D 298 MET cc_start: 0.6151 (tmt) cc_final: 0.5280 (tmt) REVERT: D 399 LYS cc_start: 0.8239 (mtmm) cc_final: 0.8015 (tptp) REVERT: D 484 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8330 (mtm) REVERT: D 581 MET cc_start: 0.8706 (mtm) cc_final: 0.8202 (mtp) REVERT: D 825 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8135 (p) REVERT: D 832 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7745 (mtmt) REVERT: D 1143 ASP cc_start: 0.8137 (t70) cc_final: 0.7918 (t70) REVERT: E 12 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7563 (ttmm) REVERT: F 260 ARG cc_start: 0.5790 (mtm180) cc_final: 0.4978 (mtp85) REVERT: F 264 LYS cc_start: 0.6227 (mptt) cc_final: 0.5998 (tptp) REVERT: F 293 GLU cc_start: 0.4715 (mp0) cc_final: 0.4272 (mp0) REVERT: F 409 ASN cc_start: 0.8916 (m-40) cc_final: 0.8537 (m-40) REVERT: F 474 MET cc_start: 0.7766 (ppp) cc_final: 0.7366 (ppp) REVERT: I 10 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: I 64 GLU cc_start: 0.7729 (pp20) cc_final: 0.7077 (pp20) REVERT: M 98 ARG cc_start: 0.4469 (pmt170) cc_final: 0.2799 (mtt180) REVERT: M 199 GLU cc_start: 0.5115 (mp0) cc_final: 0.4231 (tp30) outliers start: 87 outliers final: 62 residues processed: 429 average time/residue: 0.2063 time to fit residues: 145.4377 Evaluate side-chains 408 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 338 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 186 LYS Chi-restraints excluded: chain M residue 190 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 157 optimal weight: 7.9990 chunk 90 optimal weight: 0.0060 chunk 141 optimal weight: 7.9990 chunk 354 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 308 optimal weight: 3.9990 chunk 230 optimal weight: 0.0670 chunk 208 optimal weight: 7.9990 chunk 202 optimal weight: 0.9980 chunk 42 optimal weight: 0.0060 chunk 135 optimal weight: 8.9990 overall best weight: 1.0152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.177744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.141151 restraints weight = 50285.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.133169 restraints weight = 86070.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.130349 restraints weight = 69507.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130584 restraints weight = 64587.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.130860 restraints weight = 48525.531| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33953 Z= 0.119 Angle : 0.598 14.413 46264 Z= 0.315 Chirality : 0.043 0.243 5282 Planarity : 0.004 0.051 5664 Dihedral : 17.176 140.661 5501 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 2.19 % Allowed : 18.26 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.13), residues: 3920 helix: 0.64 (0.13), residues: 1595 sheet: -1.25 (0.24), residues: 428 loop : -2.02 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 202 TYR 0.022 0.001 TYR M 134 PHE 0.018 0.001 PHE F 316 TRP 0.015 0.001 TRP C 997 HIS 0.003 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (33947) covalent geometry : angle 0.59665 / 0.31 (46258) hydrogen bonds : bond 0.04309 / 2.79 ( 1458) hydrogen bonds : angle 4.52487 / 3.07 ( 4074) metal coordination : bond 0.00254 / 0.13 ( 6) metal coordination : angle 3.19006 / 1.94 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7840 Ramachandran restraints generated. 3920 Oldfield, 0 Emsley, 3920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 353 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7782 (tp30) cc_final: 0.7234 (mt-10) REVERT: A 62 ASP cc_start: 0.7323 (t70) cc_final: 0.6949 (t0) REVERT: A 102 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9100 (tp) REVERT: A 145 LYS cc_start: 0.8812 (tttt) cc_final: 0.8416 (tttm) REVERT: B 93 GLN cc_start: 0.6664 (tp40) cc_final: 0.5655 (mp10) REVERT: B 127 GLN cc_start: 0.7871 (pm20) cc_final: 0.7376 (pt0) REVERT: C 36 GLN cc_start: 0.7766 (tp40) cc_final: 0.7432 (tp-100) REVERT: C 163 LYS cc_start: 0.4034 (OUTLIER) cc_final: 0.3664 (pptt) REVERT: C 203 LYS cc_start: 0.8815 (ttmt) cc_final: 0.8577 (ttmm) REVERT: C 314 ASN cc_start: 0.6265 (t0) cc_final: 0.5994 (t0) REVERT: C 369 MET cc_start: 0.7939 (tmm) cc_final: 0.7625 (ttt) REVERT: C 434 ASP cc_start: 0.6271 (m-30) cc_final: 0.5702 (m-30) REVERT: C 504 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7331 (tm-30) REVERT: C 545 PHE cc_start: 0.7731 (m-80) cc_final: 0.7194 (m-10) REVERT: C 711 ASP cc_start: 0.7649 (m-30) cc_final: 0.7304 (m-30) REVERT: C 958 LYS cc_start: 0.8848 (tttm) cc_final: 0.8571 (ttpt) REVERT: C 1025 PHE cc_start: 0.6482 (t80) cc_final: 0.5958 (m-80) REVERT: C 1119 MET cc_start: 0.9066 (tpt) cc_final: 0.8581 (tpt) REVERT: D 30 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8240 (mt) REVERT: D 295 GLU cc_start: 0.7686 (tp30) cc_final: 0.6997 (tp30) REVERT: D 298 MET cc_start: 0.6119 (tmt) cc_final: 0.5307 (tmt) REVERT: D 399 LYS cc_start: 0.8221 (mtmm) cc_final: 0.8015 (tptp) REVERT: D 484 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8294 (mtm) REVERT: D 581 MET cc_start: 0.8659 (mtm) cc_final: 0.8183 (mtp) REVERT: D 747 MET cc_start: 0.6470 (pmm) cc_final: 0.6044 (pmm) REVERT: D 822 MET cc_start: 0.7662 (mmm) cc_final: 0.7315 (mmm) REVERT: D 825 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8215 (p) REVERT: D 832 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7701 (mtmt) REVERT: E 12 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7573 (ttmm) REVERT: F 260 ARG cc_start: 0.5410 (mtm180) cc_final: 0.4730 (mtp85) REVERT: F 293 GLU cc_start: 0.4731 (mp0) cc_final: 0.4144 (mp0) REVERT: F 409 ASN cc_start: 0.8806 (m-40) cc_final: 0.8364 (m-40) REVERT: F 474 MET cc_start: 0.7841 (ppp) cc_final: 0.7309 (ppp) REVERT: F 507 MET cc_start: 0.8607 (mmt) cc_final: 0.8090 (mmt) REVERT: I 10 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: I 64 GLU cc_start: 0.7715 (pp20) cc_final: 0.6526 (pp20) REVERT: M 98 ARG cc_start: 0.4184 (pmt170) cc_final: 0.2761 (mtt180) REVERT: M 199 GLU cc_start: 0.4865 (mp0) cc_final: 0.4152 (tp30) outliers start: 74 outliers final: 58 residues processed: 409 average time/residue: 0.2140 time to fit residues: 143.7432 Evaluate side-chains 403 residues out of total 3387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 337 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 530 LEU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain M residue 139 LEU Chi-restraints excluded: chain M residue 186 LYS Chi-restraints excluded: chain M residue 190 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 227 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 284 optimal weight: 20.0000 chunk 380 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 345 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.175696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138864 restraints weight = 50007.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.129514 restraints weight = 80828.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.125570 restraints weight = 73606.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126037 restraints weight = 66125.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126563 restraints weight = 49856.803| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33953 Z= 0.158 Angle : 0.620 14.079 46264 Z= 0.326 Chirality : 0.044 0.248 5282 Planarity : 0.004 0.070 5664 Dihedral : 17.131 140.883 5501 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.71 % Favored : 94.26 % Rotamer: Outliers : 2.39 % Allowed : 18.32 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.13), residues: 3920 helix: 0.64 (0.13), residues: 1592 sheet: -1.23 (0.25), residues: 418 loop : -2.02 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1034 TYR 0.029 0.001 TYR F 268 PHE 0.017 0.001 PHE F 316 TRP 0.014 0.002 TRP C 997 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (33947) covalent geometry : angle 0.61917 / 0.33 (46258) hydrogen bonds : bond 0.04521 / 2.94 ( 1458) hydrogen bonds : angle 4.53747 / 3.09 ( 4074) metal coordination : bond 0.00509 / 0.28 ( 6) metal coordination : angle 3.57791 / 2.18 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5793.22 seconds wall clock time: 100 minutes 50.96 seconds (6050.96 seconds total)