Starting phenix.real_space_refine on Sat Aug 8 07:26:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eh9_28144/08_2026/8eh9_28144.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eh9_28144/08_2026/8eh9_28144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8eh9_28144/08_2026/8eh9_28144.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eh9_28144/08_2026/8eh9_28144.cif" model { file = "/net/cci-nas-00/data/ceres_data/8eh9_28144/08_2026/8eh9_28144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eh9_28144/08_2026/8eh9_28144.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eh9_28144/08_2026/8eh9_28144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eh9_28144/08_2026/8eh9_28144.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 63 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16251 2.51 5 N 4638 2.21 5 O 5173 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26234 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 472 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 627 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "R" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNAv2': 10} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "G" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1679 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} 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: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} 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: "I" Number of atoms: 10372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10372 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 10524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10524 Classifications: {'peptide': 1358} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1302} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "K" 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: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15502 SG CYS J 70 104.968 101.810 90.315 1.00 75.93 S ATOM 15516 SG CYS J 72 104.937 105.378 91.491 1.00 83.55 S ATOM 15624 SG CYS J 85 107.256 102.920 93.205 1.00 78.54 S ATOM 15648 SG CYS J 88 103.529 102.631 93.752 1.00 80.03 S ATOM 21324 SG CYS J 814 87.665 36.514 86.912 1.00 49.61 S ATOM 21889 SG CYS J 888 86.502 40.194 87.195 1.00 40.44 S ATOM 21940 SG CYS J 895 87.305 38.777 83.766 1.00 36.22 S ATOM 21961 SG CYS J 898 84.355 37.480 85.534 1.00 33.77 S Time building chain proxies: 5.46, per 1000 atoms: 0.21 Number of scatterers: 26234 At special positions: 0 Unit cell: (140.4, 146.9, 163.8, 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 106 16.00 P 63 15.00 Mg 1 11.99 O 5173 8.00 N 4638 7.00 C 16251 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: 2.36 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " Number of angles added : 12 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5884 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 46 sheets defined 37.4% alpha, 14.9% beta 29 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 4.124A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 158 removed outlier: 3.987A pdb=" N ARG G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.741A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.923A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.906A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 40 Processing helix chain 'I' and resid 42 through 47 removed outlier: 4.236A pdb=" N GLY I 45 " --> pdb=" O ASP I 42 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR I 47 " --> pdb=" O GLU I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.577A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 295 removed outlier: 3.752A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 329 Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.822A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 451 Processing helix chain 'I' and resid 455 through 480 removed outlier: 3.762A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 removed outlier: 3.832A pdb=" N SER I 499 " --> pdb=" O ALA I 495 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 removed outlier: 3.574A pdb=" N ARG I 528 " --> pdb=" O ILE I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 544 through 549 removed outlier: 3.980A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP I 549 " --> pdb=" O PHE I 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 544 through 549' Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.748A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 614 removed outlier: 4.144A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 609 through 614' Processing helix chain 'I' and resid 656 through 660 removed outlier: 3.685A pdb=" N VAL I 660 " --> pdb=" O THR I 657 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.697A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 664 through 668' Processing helix chain 'I' and resid 676 through 688 removed outlier: 3.859A pdb=" N MET I 681 " --> pdb=" O ASN I 677 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY I 682 " --> pdb=" O ARG I 678 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 942 through 980 Processing helix chain 'I' and resid 987 through 992 removed outlier: 4.225A pdb=" N LYS I 991 " --> pdb=" O GLU I 987 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.513A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.605A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.795A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.938A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1169 through 1176 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.673A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1280 removed outlier: 3.825A pdb=" N TRP I1276 " --> pdb=" O GLU I1272 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA I1277 " --> pdb=" O MET I1273 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU I1278 " --> pdb=" O GLU I1274 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.513A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1298 through 1309 removed outlier: 3.584A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.532A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 95 through 100 removed outlier: 3.708A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 117 Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.916A pdb=" N LEU J 374 " --> pdb=" O LYS J 370 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 403 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.517A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP J 413 " --> pdb=" O TRP J 409 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU J 414 " --> pdb=" O ASP J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 505 through 514 Processing helix chain 'J' and resid 529 through 540 Processing helix chain 'J' and resid 573 through 581 removed outlier: 3.799A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 removed outlier: 3.860A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 634 removed outlier: 3.789A pdb=" N TYR J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 704 removed outlier: 3.521A pdb=" N ASP J 684 " --> pdb=" O ASN J 680 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU J 704 " --> pdb=" O ASN J 700 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 removed outlier: 3.955A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 770 through 790 removed outlier: 3.894A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU J 783 " --> pdb=" O ALA J 779 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU J 788 " --> pdb=" O ALA J 784 " (cutoff:3.500A) Processing helix chain 'J' and resid 790 through 804 removed outlier: 4.069A pdb=" N LEU J 796 " --> pdb=" O ASN J 792 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL J 803 " --> pdb=" O ARG J 799 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 884 through 888 removed outlier: 3.758A pdb=" N CYS J 888 " --> pdb=" O VAL J 885 " (cutoff:3.500A) Processing helix chain 'J' and resid 914 through 925 removed outlier: 4.058A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 932 Processing helix chain 'J' and resid 1069 through 1074 removed outlier: 4.130A pdb=" N ASP J1073 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1139 through 1147 Processing helix chain 'J' and resid 1218 through 1243 removed outlier: 7.817A pdb=" N VAL J1226 " --> pdb=" O ARG J1222 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N HIS J1227 " --> pdb=" O LEU J1223 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA J1228 " --> pdb=" O ARG J1224 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.434A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.558A pdb=" N ASN J1295 " --> pdb=" O GLU J1291 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.844A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 3.642A pdb=" N GLU J1334 " --> pdb=" O ARG J1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1362 through 1372 Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.580A pdb=" N VAL K 32 " --> pdb=" O ARG K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 removed outlier: 3.522A pdb=" N ILE K 49 " --> pdb=" O LYS K 45 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY K 57 " --> pdb=" O GLU K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 78 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.221A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU G 188 " --> pdb=" O LYS G 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 97 through 99 removed outlier: 3.902A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 102 through 104 removed outlier: 3.625A pdb=" N LYS G 104 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE G 140 " --> pdb=" O LYS G 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 4.022A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 151 through 153 removed outlier: 3.569A pdb=" N VAL G 153 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 12 through 15 removed outlier: 7.578A pdb=" N THR H 27 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA H 190 " --> pdb=" O LEU H 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 97 through 101 removed outlier: 3.787A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 111 removed outlier: 6.417A pdb=" N GLY H 108 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N HIS H 132 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 removed outlier: 3.865A pdb=" N VAL H 153 " --> pdb=" O ALA H 175 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA H 175 " --> pdb=" O VAL H 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'I' and resid 59 through 60 Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 7.584A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 147 through 148 removed outlier: 6.122A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB8, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.066A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 301 through 302 Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.658A pdb=" N GLU I 588 " --> pdb=" O GLN I 580 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.658A pdb=" N GLU I 588 " --> pdb=" O GLN I 580 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 616 through 617 Processing sheet with id=AC5, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.819A pdb=" N ASP I 749 " --> pdb=" O ILE I 734 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 757 through 758 removed outlier: 3.591A pdb=" N THR I 757 " --> pdb=" O ILE I 765 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE I 765 " --> pdb=" O THR I 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AC8, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 3.539A pdb=" N ALA I1067 " --> pdb=" O LEU I1233 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN I 798 " --> pdb=" O MET I1232 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 830 through 839 removed outlier: 3.598A pdb=" N GLN I 834 " --> pdb=" O LEU I1054 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL I1050 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 882 through 884 removed outlier: 7.405A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD3, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.520A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AD5, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AD6, first strand: chain 'J' and resid 103 through 112 removed outlier: 10.397A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.654A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 144 through 145 Processing sheet with id=AD8, first strand: chain 'J' and resid 526 through 527 removed outlier: 7.556A pdb=" N LEU J 527 " --> pdb=" O ARG J 551 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 555 through 556 Processing sheet with id=AE1, first strand: chain 'J' and resid 707 through 708 Processing sheet with id=AE2, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain 'J' and resid 821 through 822 removed outlier: 3.548A pdb=" N VAL J 880 " --> pdb=" O MET J 822 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 949 through 952 removed outlier: 4.375A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL J 952 " --> pdb=" O THR J1016 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N THR J1016 " --> pdb=" O VAL J 952 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.717A pdb=" N LYS J 983 " --> pdb=" O LYS J 959 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER J 961 " --> pdb=" O GLU J 981 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1026 through 1028 removed outlier: 7.019A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 3.702A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR J1038 " --> pdb=" O ALA J1077 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA J1077 " --> pdb=" O THR J1038 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1046 through 1047 Processing sheet with id=AE9, first strand: chain 'J' and resid 1187 through 1190 Processing sheet with id=AF1, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 3.687A pdb=" N VAL J1280 " --> pdb=" O ALA J1264 " (cutoff:3.500A) 963 hydrogen bonds defined for protein. 2670 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 5.97 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8704 1.34 - 1.46: 5281 1.46 - 1.58: 12457 1.58 - 1.70: 127 1.70 - 1.83: 187 Bond restraints: 26756 Sorted by residual: bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.827 -0.295 2.00e-02 2.50e+03 2.17e+02 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.730 -0.198 2.00e-02 2.50e+03 9.85e+01 bond pdb=" C7 1N7 I1401 " pdb=" C8 1N7 I1401 " ideal model delta sigma weight residual 1.542 1.707 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" C19 1N7 I1401 " pdb=" C2 1N7 I1401 " ideal model delta sigma weight residual 1.551 1.400 0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" C4 1N7 I1401 " pdb=" C5 1N7 I1401 " ideal model delta sigma weight residual 1.534 1.397 0.137 2.00e-02 2.50e+03 4.72e+01 ... (remaining 26751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 35984 2.77 - 5.55: 378 5.55 - 8.32: 45 8.32 - 11.09: 11 11.09 - 13.86: 2 Bond angle restraints: 36420 Sorted by residual: angle pdb=" C ARG J 709 " pdb=" N ASP J 710 " pdb=" CA ASP J 710 " ideal model delta sigma weight residual 121.54 131.70 -10.16 1.91e+00 2.74e-01 2.83e+01 angle pdb=" O4' DC B 18 " pdb=" C4' DC B 18 " pdb=" C3' DC B 18 " ideal model delta sigma weight residual 106.00 102.88 3.12 6.00e-01 2.78e+00 2.71e+01 angle pdb=" N GLN J 504 " pdb=" CA GLN J 504 " pdb=" CB GLN J 504 " ideal model delta sigma weight residual 114.17 108.27 5.90 1.14e+00 7.69e-01 2.68e+01 angle pdb=" O4' DG B 17 " pdb=" C4' DG B 17 " pdb=" C3' DG B 17 " ideal model delta sigma weight residual 106.00 103.17 2.83 6.00e-01 2.78e+00 2.23e+01 angle pdb=" N3 DT A 26 " pdb=" C4 DT A 26 " pdb=" O4 DT A 26 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 ... (remaining 36415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 15750 35.79 - 71.58: 490 71.58 - 107.37: 37 107.37 - 143.16: 1 143.16 - 178.95: 1 Dihedral angle restraints: 16279 sinusoidal: 7128 harmonic: 9151 Sorted by residual: dihedral pdb=" CA LEU J1138 " pdb=" C LEU J1138 " pdb=" N PRO J1139 " pdb=" CA PRO J1139 " ideal model delta harmonic sigma weight residual 180.00 145.64 34.36 0 5.00e+00 4.00e-02 4.72e+01 dihedral pdb=" CA GLU J 925 " pdb=" C GLU J 925 " pdb=" N PRO J 926 " pdb=" CA PRO J 926 " ideal model delta harmonic sigma weight residual 180.00 147.93 32.07 0 5.00e+00 4.00e-02 4.11e+01 dihedral pdb=" O5' U R 12 " pdb=" C5' U R 12 " pdb=" C4' U R 12 " pdb=" C3' U R 12 " ideal model delta sinusoidal sigma weight residual 180.00 142.01 37.99 3 6.40e+00 2.44e-02 3.66e+01 ... (remaining 16276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3797 0.083 - 0.166: 355 0.166 - 0.248: 21 0.248 - 0.331: 2 0.331 - 0.414: 1 Chirality restraints: 4176 Sorted by residual: chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.95 0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" CB ILE K 13 " pdb=" CA ILE K 13 " pdb=" CG1 ILE K 13 " pdb=" CG2 ILE K 13 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C5 1N7 I1401 " pdb=" C4 1N7 I1401 " pdb=" C6 1N7 I1401 " pdb=" C9 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.85 -2.59 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 4173 not shown) Planarity restraints: 4541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU J 925 " -0.061 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO J 926 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO J 926 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO J 926 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J1138 " 0.047 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO J1139 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO J1139 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO J1139 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 69 " 0.199 9.50e-02 1.11e+02 8.94e-02 5.80e+00 pdb=" NE ARG K 69 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG K 69 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG K 69 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG K 69 " 0.002 2.00e-02 2.50e+03 ... (remaining 4538 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 275 2.60 - 3.18: 21971 3.18 - 3.75: 40907 3.75 - 4.33: 54329 4.33 - 4.90: 89990 Nonbonded interactions: 207472 Sorted by model distance: nonbonded pdb=" O3' C R 18 " pdb="MG MG R 101 " model vdw 2.026 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG R 101 " model vdw 2.079 2.170 nonbonded pdb=" O5' U R 19 " pdb="MG MG R 101 " model vdw 2.154 2.170 nonbonded pdb=" O TRP J 115 " pdb=" OG SER J 119 " model vdw 2.209 3.040 nonbonded pdb=" OD2 ASP J 460 " pdb="MG MG R 101 " model vdw 2.213 2.170 ... (remaining 207467 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 'G' 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 231)) selection = (chain 'H' 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 231)) } 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: 1.450 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 30.140 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 : 0.005 0.295 26764 Z= 0.277 Angle : 0.765 13.865 36432 Z= 0.451 Chirality : 0.048 0.414 4176 Planarity : 0.005 0.092 4541 Dihedral : 16.462 178.948 10395 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.04 % Allowed : 0.33 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.89 (0.14), residues: 3174 helix: 0.09 (0.16), residues: 1081 sheet: -2.25 (0.26), residues: 362 loop : -1.96 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 69 TYR 0.027 0.001 TYR I 395 PHE 0.026 0.001 PHE I1025 TRP 0.020 0.002 TRP J 236 HIS 0.007 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.28 (26756) covalent geometry : angle 0.76344 / 0.45 (36420) hydrogen bonds : bond 0.18486 / 19.98 ( 1030) hydrogen bonds : angle 6.84255 / 6.62 ( 2818) metal coordination : bond 0.00377 / 0.35 ( 8) metal coordination : angle 2.46938 / 4.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 474 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 41 ASN cc_start: 0.8074 (t0) cc_final: 0.7412 (t0) REVERT: I 68 LEU cc_start: 0.8208 (tp) cc_final: 0.7983 (tt) REVERT: I 85 CYS cc_start: 0.8618 (m) cc_final: 0.8388 (m) REVERT: I 427 ASP cc_start: 0.7841 (m-30) cc_final: 0.7378 (m-30) REVERT: I 468 LEU cc_start: 0.8811 (tp) cc_final: 0.8373 (tp) REVERT: I 834 GLN cc_start: 0.8073 (pt0) cc_final: 0.7745 (pt0) REVERT: I 1248 THR cc_start: 0.8022 (t) cc_final: 0.7623 (t) REVERT: J 151 MET cc_start: 0.7174 (mpp) cc_final: 0.6715 (ppp) REVERT: J 382 TYR cc_start: 0.9024 (m-10) cc_final: 0.8779 (m-10) REVERT: J 466 MET cc_start: 0.7910 (mtp) cc_final: 0.7668 (mtm) REVERT: J 679 TYR cc_start: 0.6991 (t80) cc_final: 0.6772 (t80) REVERT: J 697 MET cc_start: 0.6771 (tmm) cc_final: 0.6261 (tmm) REVERT: J 806 ASP cc_start: 0.7517 (p0) cc_final: 0.6721 (p0) REVERT: J 1258 ARG cc_start: 0.8125 (ttt90) cc_final: 0.7607 (ttt90) REVERT: K 68 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8253 (mm-30) outliers start: 1 outliers final: 0 residues processed: 475 average time/residue: 0.1742 time to fit residues: 134.7840 Evaluate side-chains 341 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.0270 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 8.9990 overall best weight: 2.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 147 GLN I 165 HIS ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 922 ASN I1220 GLN J 424 ASN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 817 HIS J1049 GLN J1126 GLN J1197 ASN J1326 GLN J1366 HIS K 15 ASN K 31 GLN K 62 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.128986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.103749 restraints weight = 50301.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.103657 restraints weight = 32028.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.104091 restraints weight = 26466.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.104782 restraints weight = 23999.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.104831 restraints weight = 21034.867| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26764 Z= 0.189 Angle : 0.668 11.195 36432 Z= 0.347 Chirality : 0.045 0.241 4176 Planarity : 0.005 0.103 4541 Dihedral : 13.827 178.562 4198 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.37 % Allowed : 10.55 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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 (0.14), residues: 3174 helix: 0.38 (0.16), residues: 1109 sheet: -1.92 (0.27), residues: 361 loop : -1.90 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I1246 TYR 0.014 0.001 TYR H 68 PHE 0.021 0.001 PHE J 260 TRP 0.010 0.001 TRP J 115 HIS 0.008 0.001 HIS J 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (26756) covalent geometry : angle 0.66678 / 0.35 (36420) hydrogen bonds : bond 0.04741 / 5.32 ( 1030) hydrogen bonds : angle 5.33102 / 5.38 ( 2818) metal coordination : bond 0.00883 / 0.84 ( 8) metal coordination : angle 2.50987 / 4.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 366 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 68 LEU cc_start: 0.8502 (tp) cc_final: 0.8247 (tp) REVERT: I 85 CYS cc_start: 0.8945 (m) cc_final: 0.8617 (m) REVERT: I 108 GLU cc_start: 0.5676 (mm-30) cc_final: 0.5433 (mm-30) REVERT: I 311 CYS cc_start: 0.6766 (p) cc_final: 0.6362 (p) REVERT: I 472 GLU cc_start: 0.8410 (tp30) cc_final: 0.8141 (tp30) REVERT: I 527 LYS cc_start: 0.9370 (mttt) cc_final: 0.9047 (mtmm) REVERT: I 930 ASP cc_start: 0.8462 (t70) cc_final: 0.8155 (t0) REVERT: I 1119 MET cc_start: 0.8416 (tpp) cc_final: 0.8171 (tpp) REVERT: I 1204 LEU cc_start: 0.9002 (mt) cc_final: 0.8156 (mt) REVERT: I 1329 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7472 (mt-10) REVERT: J 264 ASP cc_start: 0.7819 (m-30) cc_final: 0.7587 (m-30) REVERT: J 382 TYR cc_start: 0.9191 (m-10) cc_final: 0.8927 (m-10) REVERT: J 697 MET cc_start: 0.6278 (tmm) cc_final: 0.5770 (tmm) REVERT: J 806 ASP cc_start: 0.7703 (p0) cc_final: 0.6904 (p0) REVERT: J 925 GLU cc_start: 0.8765 (pp20) cc_final: 0.8418 (pp20) outliers start: 37 outliers final: 18 residues processed: 386 average time/residue: 0.1648 time to fit residues: 103.5942 Evaluate side-chains 345 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 327 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 837 ASP Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1184 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 282 optimal weight: 20.0000 chunk 73 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 273 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 294 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 165 HIS ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 922 ASN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1049 GLN J1366 HIS ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.129294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.104044 restraints weight = 50259.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.104009 restraints weight = 32244.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.104589 restraints weight = 27084.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.105440 restraints weight = 23422.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.105327 restraints weight = 20138.310| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26764 Z= 0.146 Angle : 0.612 9.934 36432 Z= 0.318 Chirality : 0.044 0.263 4176 Planarity : 0.004 0.086 4541 Dihedral : 13.778 177.962 4198 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.55 % Allowed : 13.33 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.38 (0.15), residues: 3174 helix: 0.60 (0.16), residues: 1112 sheet: -1.78 (0.27), residues: 360 loop : -1.81 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 709 TYR 0.017 0.001 TYR J 165 PHE 0.013 0.001 PHE I1025 TRP 0.008 0.001 TRP J 115 HIS 0.008 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (26756) covalent geometry : angle 0.61149 / 0.32 (36420) hydrogen bonds : bond 0.04158 / 4.66 ( 1030) hydrogen bonds : angle 4.97260 / 5.06 ( 2818) metal coordination : bond 0.00633 / 0.59 ( 8) metal coordination : angle 1.99548 / 3.57 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 359 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8063 (ptmt) REVERT: H 185 TYR cc_start: 0.8949 (p90) cc_final: 0.8517 (p90) REVERT: H 206 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6683 (tm-30) REVERT: I 68 LEU cc_start: 0.8402 (tp) cc_final: 0.8148 (tp) REVERT: I 85 CYS cc_start: 0.8838 (m) cc_final: 0.8502 (m) REVERT: I 108 GLU cc_start: 0.5623 (mm-30) cc_final: 0.5407 (mm-30) REVERT: I 274 ILE cc_start: 0.6838 (OUTLIER) cc_final: 0.6525 (tt) REVERT: I 472 GLU cc_start: 0.8387 (tp30) cc_final: 0.8142 (tp30) REVERT: I 527 LYS cc_start: 0.9360 (mttt) cc_final: 0.9017 (mtmm) REVERT: I 728 ASP cc_start: 0.7657 (t0) cc_final: 0.7248 (t0) REVERT: I 930 ASP cc_start: 0.8350 (t70) cc_final: 0.8117 (t0) REVERT: I 1119 MET cc_start: 0.8341 (tpp) cc_final: 0.8056 (tpp) REVERT: I 1204 LEU cc_start: 0.8868 (mt) cc_final: 0.8008 (mt) REVERT: I 1279 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8186 (mt-10) REVERT: J 133 ARG cc_start: 0.8489 (mmm-85) cc_final: 0.8018 (mmt90) REVERT: J 135 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8878 (tt) REVERT: J 169 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.7983 (tt) REVERT: J 382 TYR cc_start: 0.9137 (m-10) cc_final: 0.8871 (m-10) REVERT: J 697 MET cc_start: 0.6662 (tmm) cc_final: 0.6184 (tmm) REVERT: J 806 ASP cc_start: 0.7427 (p0) cc_final: 0.6625 (p0) REVERT: J 807 LEU cc_start: 0.9172 (tt) cc_final: 0.8924 (tt) REVERT: J 925 GLU cc_start: 0.8644 (pp20) cc_final: 0.8276 (pp20) REVERT: J 1152 GLU cc_start: 0.7257 (mp0) cc_final: 0.6976 (mp0) REVERT: J 1236 GLU cc_start: 0.6284 (tp30) cc_final: 0.6003 (tp30) REVERT: K 60 ASN cc_start: 0.7642 (p0) cc_final: 0.7329 (p0) outliers start: 42 outliers final: 27 residues processed: 380 average time/residue: 0.1461 time to fit residues: 91.6409 Evaluate side-chains 359 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 329 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 415 VAL Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1184 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 257 optimal weight: 3.9990 chunk 6 optimal weight: 0.0980 chunk 223 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 303 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 chunk 315 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 147 GLN H 147 GLN I 165 HIS ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN I 922 ASN J 341 ASN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1049 GLN J1326 GLN J1366 HIS K 31 GLN K 62 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.130877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.105420 restraints weight = 49759.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.106015 restraints weight = 31997.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.106339 restraints weight = 24682.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106910 restraints weight = 22846.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.107047 restraints weight = 20367.997| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26764 Z= 0.115 Angle : 0.588 10.357 36432 Z= 0.304 Chirality : 0.043 0.266 4176 Planarity : 0.004 0.083 4541 Dihedral : 13.693 177.655 4198 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.00 % Allowed : 14.81 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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 (0.15), residues: 3174 helix: 0.73 (0.16), residues: 1112 sheet: -1.54 (0.28), residues: 359 loop : -1.74 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J1036 TYR 0.014 0.001 TYR J 165 PHE 0.014 0.001 PHE I 812 TRP 0.006 0.001 TRP J 115 HIS 0.010 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (26756) covalent geometry : angle 0.58760 / 0.30 (36420) hydrogen bonds : bond 0.03787 / 4.24 ( 1030) hydrogen bonds : angle 4.74183 / 4.84 ( 2818) metal coordination : bond 0.00415 / 0.37 ( 8) metal coordination : angle 1.76205 / 3.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 375 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 185 TYR cc_start: 0.8390 (p90) cc_final: 0.7982 (p90) REVERT: G 200 LYS cc_start: 0.8510 (ttmt) cc_final: 0.8059 (ptmt) REVERT: H 41 ASN cc_start: 0.8621 (t0) cc_final: 0.8014 (t0) REVERT: H 147 GLN cc_start: 0.8220 (mt0) cc_final: 0.7918 (mm110) REVERT: H 185 TYR cc_start: 0.9027 (p90) cc_final: 0.8632 (p90) REVERT: H 206 GLU cc_start: 0.7032 (tm-30) cc_final: 0.6593 (tm-30) REVERT: I 68 LEU cc_start: 0.8427 (tp) cc_final: 0.8187 (tp) REVERT: I 85 CYS cc_start: 0.8830 (m) cc_final: 0.8441 (m) REVERT: I 274 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6515 (tt) REVERT: I 527 LYS cc_start: 0.9284 (mttt) cc_final: 0.8989 (mtmm) REVERT: I 728 ASP cc_start: 0.7609 (t0) cc_final: 0.7183 (t0) REVERT: I 834 GLN cc_start: 0.8109 (pt0) cc_final: 0.7802 (pt0) REVERT: I 1066 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.8023 (mtm) REVERT: I 1119 MET cc_start: 0.8290 (tpp) cc_final: 0.8032 (tpp) REVERT: I 1204 LEU cc_start: 0.9000 (mt) cc_final: 0.8194 (mt) REVERT: I 1279 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8065 (mt-10) REVERT: J 133 ARG cc_start: 0.8537 (mmm-85) cc_final: 0.8075 (mmt90) REVERT: J 169 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7865 (tt) REVERT: J 382 TYR cc_start: 0.9081 (m-10) cc_final: 0.8722 (m-10) REVERT: J 697 MET cc_start: 0.6553 (tmm) cc_final: 0.6087 (tmm) REVERT: J 806 ASP cc_start: 0.7303 (p0) cc_final: 0.6610 (p0) REVERT: J 925 GLU cc_start: 0.8575 (pp20) cc_final: 0.8200 (pp20) REVERT: J 1254 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7676 (mt-10) REVERT: K 8 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.7994 (p0) REVERT: K 29 GLN cc_start: 0.7738 (mt0) cc_final: 0.7507 (mt0) REVERT: K 60 ASN cc_start: 0.7585 (p0) cc_final: 0.7385 (p0) outliers start: 54 outliers final: 27 residues processed: 410 average time/residue: 0.1500 time to fit residues: 102.0731 Evaluate side-chains 360 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 329 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain K residue 8 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 199 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 262 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 291 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 316 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 147 GLN I 165 HIS ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 922 ASN J 341 ASN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1049 GLN ** J1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.125751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.100581 restraints weight = 50041.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.100444 restraints weight = 31784.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.100839 restraints weight = 27843.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.101238 restraints weight = 25819.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.101509 restraints weight = 22902.281| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 26764 Z= 0.237 Angle : 0.675 10.167 36432 Z= 0.346 Chirality : 0.045 0.269 4176 Planarity : 0.005 0.087 4541 Dihedral : 13.764 176.130 4198 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.67 % Allowed : 16.48 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.28 (0.15), residues: 3174 helix: 0.69 (0.16), residues: 1100 sheet: -1.56 (0.27), residues: 377 loop : -1.77 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 26 TYR 0.015 0.002 TYR J 772 PHE 0.013 0.002 PHE I 405 TRP 0.007 0.001 TRP J 236 HIS 0.010 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.24 (26756) covalent geometry : angle 0.67462 / 0.35 (36420) hydrogen bonds : bond 0.04100 / 4.62 ( 1030) hydrogen bonds : angle 4.81011 / 5.01 ( 2818) metal coordination : bond 0.01282 / 1.19 ( 8) metal coordination : angle 1.74765 / 3.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 329 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 185 TYR cc_start: 0.8544 (p90) cc_final: 0.8212 (p90) REVERT: G 200 LYS cc_start: 0.8654 (ttmt) cc_final: 0.8192 (ptmt) REVERT: H 185 TYR cc_start: 0.9166 (p90) cc_final: 0.8723 (p90) REVERT: I 68 LEU cc_start: 0.8423 (tp) cc_final: 0.8199 (tp) REVERT: I 85 CYS cc_start: 0.8989 (m) cc_final: 0.8606 (m) REVERT: I 274 ILE cc_start: 0.6902 (OUTLIER) cc_final: 0.6634 (tt) REVERT: I 527 LYS cc_start: 0.9326 (mttt) cc_final: 0.9089 (mtmm) REVERT: I 704 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6762 (ttm) REVERT: I 728 ASP cc_start: 0.7681 (t0) cc_final: 0.7426 (t0) REVERT: I 1066 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8307 (mtp) REVERT: J 133 ARG cc_start: 0.8556 (mmm-85) cc_final: 0.8169 (mmt90) REVERT: J 169 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7828 (tt) REVERT: J 382 TYR cc_start: 0.9146 (m-10) cc_final: 0.8845 (m-10) REVERT: J 697 MET cc_start: 0.6619 (tmm) cc_final: 0.6145 (tmm) REVERT: J 743 MET cc_start: 0.7998 (ttm) cc_final: 0.7746 (ttm) REVERT: J 788 LEU cc_start: 0.9202 (mm) cc_final: 0.8579 (tt) REVERT: J 806 ASP cc_start: 0.7577 (p0) cc_final: 0.6896 (p0) REVERT: J 902 ASP cc_start: 0.7849 (t0) cc_final: 0.7634 (t70) REVERT: J 925 GLU cc_start: 0.8668 (pp20) cc_final: 0.8384 (pp20) REVERT: K 8 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8162 (p0) REVERT: K 29 GLN cc_start: 0.8031 (mt0) cc_final: 0.7818 (mt0) REVERT: K 75 GLN cc_start: 0.8668 (pp30) cc_final: 0.8115 (pp30) outliers start: 72 outliers final: 50 residues processed: 375 average time/residue: 0.1459 time to fit residues: 91.2140 Evaluate side-chains 372 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 317 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1049 GLN Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 55 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 170 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 281 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 298 optimal weight: 10.0000 chunk 224 optimal weight: 0.9980 chunk 188 optimal weight: 9.9990 chunk 234 optimal weight: 7.9990 chunk 284 optimal weight: 6.9990 chunk 156 optimal weight: 0.9980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 165 HIS I 554 HIS ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 922 ASN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS K 31 GLN K 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.125678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.101001 restraints weight = 50038.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.100126 restraints weight = 32471.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.100836 restraints weight = 27228.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.101358 restraints weight = 24608.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.101452 restraints weight = 22258.119| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 26764 Z= 0.208 Angle : 0.650 10.553 36432 Z= 0.334 Chirality : 0.044 0.266 4176 Planarity : 0.004 0.089 4541 Dihedral : 13.769 176.390 4198 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.81 % Allowed : 17.18 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.31 (0.15), residues: 3174 helix: 0.64 (0.16), residues: 1120 sheet: -1.58 (0.27), residues: 379 loop : -1.80 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 69 TYR 0.013 0.001 TYR J 723 PHE 0.027 0.001 PHE I1025 TRP 0.006 0.001 TRP J1193 HIS 0.024 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (26756) covalent geometry : angle 0.64983 / 0.33 (36420) hydrogen bonds : bond 0.03986 / 4.47 ( 1030) hydrogen bonds : angle 4.77430 / 4.98 ( 2818) metal coordination : bond 0.01057 / 0.96 ( 8) metal coordination : angle 1.61998 / 3.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 330 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 185 TYR cc_start: 0.8534 (p90) cc_final: 0.8171 (p90) REVERT: G 200 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8202 (ptmt) REVERT: G 205 MET cc_start: 0.8998 (ptp) cc_final: 0.8707 (ttp) REVERT: I 85 CYS cc_start: 0.8988 (m) cc_final: 0.8608 (m) REVERT: I 274 ILE cc_start: 0.6875 (OUTLIER) cc_final: 0.6570 (tt) REVERT: I 315 MET cc_start: 0.7814 (ptp) cc_final: 0.7573 (ptt) REVERT: I 527 LYS cc_start: 0.9301 (mttt) cc_final: 0.9067 (mtmm) REVERT: I 728 ASP cc_start: 0.7705 (t0) cc_final: 0.7411 (t0) REVERT: I 1119 MET cc_start: 0.8537 (tpp) cc_final: 0.8039 (tpp) REVERT: I 1204 LEU cc_start: 0.9192 (mt) cc_final: 0.8837 (mt) REVERT: I 1279 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8233 (mt-10) REVERT: J 133 ARG cc_start: 0.8606 (mmm-85) cc_final: 0.8197 (mmt90) REVERT: J 169 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7792 (tt) REVERT: J 330 MET cc_start: 0.8176 (ptp) cc_final: 0.7779 (ptp) REVERT: J 382 TYR cc_start: 0.9118 (m-10) cc_final: 0.8750 (m-10) REVERT: J 697 MET cc_start: 0.6477 (tmm) cc_final: 0.6040 (tmm) REVERT: J 788 LEU cc_start: 0.9206 (mm) cc_final: 0.8512 (tt) REVERT: J 806 ASP cc_start: 0.7594 (p0) cc_final: 0.6939 (p0) REVERT: J 925 GLU cc_start: 0.8659 (pp20) cc_final: 0.8432 (pp20) REVERT: J 1030 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: K 8 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8107 (p0) REVERT: K 60 ASN cc_start: 0.7929 (p0) cc_final: 0.7564 (p0) outliers start: 76 outliers final: 55 residues processed: 383 average time/residue: 0.1353 time to fit residues: 86.4516 Evaluate side-chains 377 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 318 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 732 ILE Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1030 GLU Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 55 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 127 optimal weight: 3.9990 chunk 276 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 155 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 185 optimal weight: 9.9990 chunk 310 optimal weight: 0.6980 chunk 242 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 165 HIS I 437 ASN ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 922 ASN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.127040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101812 restraints weight = 49944.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.101821 restraints weight = 31872.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102321 restraints weight = 27381.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.102794 restraints weight = 25272.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.102867 restraints weight = 21509.242| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26764 Z= 0.156 Angle : 0.624 11.397 36432 Z= 0.319 Chirality : 0.044 0.269 4176 Planarity : 0.004 0.087 4541 Dihedral : 13.731 176.526 4198 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.74 % Allowed : 17.96 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.17 (0.15), residues: 3174 helix: 0.79 (0.16), residues: 1108 sheet: -1.51 (0.27), residues: 379 loop : -1.73 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 69 TYR 0.013 0.001 TYR J 723 PHE 0.025 0.001 PHE I1025 TRP 0.005 0.001 TRP J 115 HIS 0.028 0.001 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (26756) covalent geometry : angle 0.62299 / 0.32 (36420) hydrogen bonds : bond 0.03840 / 4.30 ( 1030) hydrogen bonds : angle 4.68074 / 4.89 ( 2818) metal coordination : bond 0.00683 / 0.60 ( 8) metal coordination : angle 1.63782 / 3.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 341 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 185 TYR cc_start: 0.8467 (p90) cc_final: 0.8055 (p90) REVERT: G 200 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8244 (ptmt) REVERT: H 147 GLN cc_start: 0.8535 (mt0) cc_final: 0.8158 (mm-40) REVERT: H 185 TYR cc_start: 0.9074 (p90) cc_final: 0.8661 (p90) REVERT: I 85 CYS cc_start: 0.8872 (m) cc_final: 0.8504 (m) REVERT: I 274 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6605 (tt) REVERT: I 459 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.7933 (mpp) REVERT: I 527 LYS cc_start: 0.9271 (mttt) cc_final: 0.9022 (mtmm) REVERT: I 704 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6633 (ttm) REVERT: I 728 ASP cc_start: 0.7678 (t0) cc_final: 0.7397 (t0) REVERT: I 813 GLU cc_start: 0.7370 (tt0) cc_final: 0.7118 (tt0) REVERT: I 1119 MET cc_start: 0.8429 (tpp) cc_final: 0.8016 (tpp) REVERT: I 1204 LEU cc_start: 0.9152 (mt) cc_final: 0.8702 (mt) REVERT: I 1279 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8013 (mt-10) REVERT: J 133 ARG cc_start: 0.8548 (mmm-85) cc_final: 0.8180 (mmt90) REVERT: J 169 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7653 (tt) REVERT: J 180 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.6680 (tmt) REVERT: J 330 MET cc_start: 0.8039 (ptp) cc_final: 0.7806 (ptp) REVERT: J 382 TYR cc_start: 0.9069 (m-10) cc_final: 0.8712 (m-10) REVERT: J 697 MET cc_start: 0.6660 (tmm) cc_final: 0.6240 (tmm) REVERT: J 788 LEU cc_start: 0.9278 (mm) cc_final: 0.8617 (tt) REVERT: J 806 ASP cc_start: 0.7460 (p0) cc_final: 0.6784 (p0) REVERT: J 925 GLU cc_start: 0.8604 (pp20) cc_final: 0.8353 (pp20) REVERT: J 1030 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: J 1334 GLU cc_start: 0.8050 (tp30) cc_final: 0.7846 (tp30) REVERT: K 8 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8087 (p0) REVERT: K 60 ASN cc_start: 0.8000 (p0) cc_final: 0.7587 (p0) REVERT: K 75 GLN cc_start: 0.8440 (pp30) cc_final: 0.8211 (pp30) outliers start: 74 outliers final: 53 residues processed: 388 average time/residue: 0.1528 time to fit residues: 99.0208 Evaluate side-chains 376 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 316 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 459 MET Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1030 GLU Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 55 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 175 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 295 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 216 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 2 optimal weight: 30.0000 chunk 156 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 834 GLN I 922 ASN I 965 GLN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.125737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.100754 restraints weight = 50025.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.100254 restraints weight = 31191.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.100721 restraints weight = 27536.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.101277 restraints weight = 24229.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.101510 restraints weight = 20940.211| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26764 Z= 0.163 Angle : 0.634 11.866 36432 Z= 0.322 Chirality : 0.044 0.275 4176 Planarity : 0.004 0.087 4541 Dihedral : 13.721 176.053 4198 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.70 % Allowed : 18.44 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.14 (0.15), residues: 3174 helix: 0.83 (0.16), residues: 1102 sheet: -1.45 (0.27), residues: 378 loop : -1.73 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 26 TYR 0.016 0.001 TYR I 3 PHE 0.025 0.001 PHE I1025 TRP 0.006 0.001 TRP J 580 HIS 0.015 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (26756) covalent geometry : angle 0.63350 / 0.32 (36420) hydrogen bonds : bond 0.03796 / 4.26 ( 1030) hydrogen bonds : angle 4.64231 / 4.86 ( 2818) metal coordination : bond 0.00748 / 0.68 ( 8) metal coordination : angle 1.72939 / 3.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 333 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 185 TYR cc_start: 0.8495 (p90) cc_final: 0.8051 (p90) REVERT: G 200 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8171 (ptmt) REVERT: H 147 GLN cc_start: 0.8492 (mt0) cc_final: 0.8137 (mm110) REVERT: H 185 TYR cc_start: 0.9208 (p90) cc_final: 0.8795 (p90) REVERT: I 85 CYS cc_start: 0.8983 (m) cc_final: 0.8574 (m) REVERT: I 274 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6567 (tt) REVERT: I 459 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.7929 (mpp) REVERT: I 527 LYS cc_start: 0.9250 (mttt) cc_final: 0.8990 (mtmm) REVERT: I 685 MET cc_start: 0.8264 (mtm) cc_final: 0.8016 (mtt) REVERT: I 704 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6760 (ttm) REVERT: I 728 ASP cc_start: 0.7677 (t0) cc_final: 0.7367 (t0) REVERT: I 813 GLU cc_start: 0.7533 (tt0) cc_final: 0.7260 (tt0) REVERT: I 1119 MET cc_start: 0.8486 (tpp) cc_final: 0.8092 (tpp) REVERT: I 1204 LEU cc_start: 0.9196 (mt) cc_final: 0.8608 (mt) REVERT: I 1279 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8136 (mt-10) REVERT: J 133 ARG cc_start: 0.8624 (mmm-85) cc_final: 0.8204 (mmt90) REVERT: J 136 GLU cc_start: 0.8507 (pp20) cc_final: 0.8030 (pp20) REVERT: J 169 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7744 (tt) REVERT: J 180 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.6694 (tmt) REVERT: J 330 MET cc_start: 0.8266 (ptp) cc_final: 0.8045 (ptp) REVERT: J 382 TYR cc_start: 0.9060 (m-10) cc_final: 0.8715 (m-10) REVERT: J 697 MET cc_start: 0.6492 (tmm) cc_final: 0.6108 (tmm) REVERT: J 788 LEU cc_start: 0.9253 (mm) cc_final: 0.8564 (tt) REVERT: J 806 ASP cc_start: 0.7579 (p0) cc_final: 0.6893 (p0) REVERT: J 822 MET cc_start: 0.8304 (tpp) cc_final: 0.8060 (tpt) REVERT: J 902 ASP cc_start: 0.8141 (t70) cc_final: 0.7853 (t70) REVERT: J 925 GLU cc_start: 0.8646 (pp20) cc_final: 0.8415 (pp20) REVERT: J 1030 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: J 1260 MET cc_start: 0.8677 (mtt) cc_final: 0.8398 (mtt) REVERT: K 8 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8110 (p0) REVERT: K 60 ASN cc_start: 0.7896 (p0) cc_final: 0.7672 (p0) REVERT: K 75 GLN cc_start: 0.8530 (pp30) cc_final: 0.8209 (pp30) outliers start: 73 outliers final: 56 residues processed: 382 average time/residue: 0.1382 time to fit residues: 88.3601 Evaluate side-chains 385 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 322 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 459 MET Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1030 GLU Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 55 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 113 optimal weight: 4.9990 chunk 287 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 244 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 186 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 252 optimal weight: 8.9990 chunk 297 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 ASN ** 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 = 0.3555 r_free = 0.3555 target = 0.124745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.099665 restraints weight = 50455.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.098930 restraints weight = 34354.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.099440 restraints weight = 30366.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.099901 restraints weight = 25510.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.100212 restraints weight = 22925.846| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 26764 Z= 0.218 Angle : 0.674 13.144 36432 Z= 0.343 Chirality : 0.045 0.270 4176 Planarity : 0.004 0.087 4541 Dihedral : 13.781 175.521 4198 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.96 % Allowed : 18.70 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.24 (0.15), residues: 3174 helix: 0.72 (0.16), residues: 1103 sheet: -1.50 (0.27), residues: 378 loop : -1.76 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG K 69 TYR 0.015 0.002 TYR J 772 PHE 0.026 0.001 PHE I1025 TRP 0.009 0.001 TRP J1193 HIS 0.005 0.001 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (26756) covalent geometry : angle 0.67369 / 0.34 (36420) hydrogen bonds : bond 0.03956 / 4.46 ( 1030) hydrogen bonds : angle 4.72776 / 5.01 ( 2818) metal coordination : bond 0.01127 / 1.01 ( 8) metal coordination : angle 1.85952 / 3.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 330 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 185 TYR cc_start: 0.8544 (p90) cc_final: 0.8132 (p90) REVERT: G 200 LYS cc_start: 0.8674 (ttmt) cc_final: 0.8191 (ptmt) REVERT: G 205 MET cc_start: 0.8982 (ptp) cc_final: 0.8682 (ttp) REVERT: H 147 GLN cc_start: 0.8454 (mt0) cc_final: 0.8159 (mm110) REVERT: H 185 TYR cc_start: 0.9236 (p90) cc_final: 0.8859 (p90) REVERT: I 85 CYS cc_start: 0.8993 (m) cc_final: 0.8608 (m) REVERT: I 274 ILE cc_start: 0.6927 (OUTLIER) cc_final: 0.6578 (tt) REVERT: I 459 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.7924 (mpp) REVERT: I 527 LYS cc_start: 0.9281 (mttt) cc_final: 0.9015 (mtmm) REVERT: I 685 MET cc_start: 0.8326 (mtm) cc_final: 0.8060 (mtt) REVERT: I 704 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6803 (ttm) REVERT: I 728 ASP cc_start: 0.7682 (t0) cc_final: 0.7353 (t0) REVERT: I 813 GLU cc_start: 0.7445 (tt0) cc_final: 0.7196 (tt0) REVERT: I 1119 MET cc_start: 0.8492 (tpp) cc_final: 0.8079 (tpp) REVERT: I 1204 LEU cc_start: 0.9244 (mt) cc_final: 0.8788 (mt) REVERT: I 1279 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8161 (mt-10) REVERT: J 133 ARG cc_start: 0.8634 (mmm-85) cc_final: 0.7972 (mmt90) REVERT: J 169 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7919 (pp) REVERT: J 180 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.6700 (tmt) REVERT: J 330 MET cc_start: 0.8370 (ptp) cc_final: 0.8155 (ptp) REVERT: J 382 TYR cc_start: 0.9089 (m-10) cc_final: 0.8852 (m-10) REVERT: J 697 MET cc_start: 0.6599 (tmm) cc_final: 0.6206 (tmm) REVERT: J 788 LEU cc_start: 0.9218 (mm) cc_final: 0.8567 (tt) REVERT: J 806 ASP cc_start: 0.7613 (p0) cc_final: 0.6942 (p0) REVERT: J 822 MET cc_start: 0.8310 (tpp) cc_final: 0.8064 (tpt) REVERT: J 902 ASP cc_start: 0.8204 (t70) cc_final: 0.7850 (t70) REVERT: J 925 GLU cc_start: 0.8652 (pp20) cc_final: 0.8418 (pp20) REVERT: J 1030 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: J 1260 MET cc_start: 0.8724 (mtt) cc_final: 0.8471 (mtt) REVERT: K 8 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8129 (p0) REVERT: K 60 ASN cc_start: 0.7956 (p0) cc_final: 0.7693 (p0) REVERT: K 75 GLN cc_start: 0.8518 (pp30) cc_final: 0.8174 (pp30) outliers start: 80 outliers final: 64 residues processed: 384 average time/residue: 0.1358 time to fit residues: 87.1017 Evaluate side-chains 386 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 315 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 459 MET Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1030 GLU Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 55 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 292 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 chunk 290 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 129 optimal weight: 0.6980 chunk 212 optimal weight: 0.7980 chunk 295 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 ASN ** 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 = 0.3580 r_free = 0.3580 target = 0.126515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.101431 restraints weight = 49822.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.101217 restraints weight = 31138.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.101732 restraints weight = 27008.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.102161 restraints weight = 23765.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.102248 restraints weight = 20967.254| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26764 Z= 0.155 Angle : 0.653 16.428 36432 Z= 0.330 Chirality : 0.044 0.271 4176 Planarity : 0.004 0.088 4541 Dihedral : 13.754 176.083 4198 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.63 % Allowed : 19.47 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.17 (0.15), residues: 3174 helix: 0.80 (0.16), residues: 1104 sheet: -1.50 (0.27), residues: 376 loop : -1.72 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 994 TYR 0.013 0.001 TYR H 68 PHE 0.025 0.001 PHE I1025 TRP 0.006 0.001 TRP J1193 HIS 0.007 0.001 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (26756) covalent geometry : angle 0.65238 / 0.33 (36420) hydrogen bonds : bond 0.03781 / 4.24 ( 1030) hydrogen bonds : angle 4.65416 / 4.90 ( 2818) metal coordination : bond 0.00666 / 0.58 ( 8) metal coordination : angle 1.80303 / 3.44 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 332 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8302 (ptmt) REVERT: H 147 GLN cc_start: 0.8353 (mt0) cc_final: 0.8105 (mm110) REVERT: H 185 TYR cc_start: 0.9180 (p90) cc_final: 0.8858 (p90) REVERT: I 85 CYS cc_start: 0.8871 (m) cc_final: 0.8481 (m) REVERT: I 274 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6566 (tt) REVERT: I 322 LEU cc_start: 0.8230 (mt) cc_final: 0.8015 (pp) REVERT: I 459 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.7903 (mpp) REVERT: I 527 LYS cc_start: 0.9245 (mttt) cc_final: 0.9001 (mtmm) REVERT: I 685 MET cc_start: 0.8178 (mtm) cc_final: 0.7943 (mtt) REVERT: I 704 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6788 (ttm) REVERT: I 813 GLU cc_start: 0.7406 (tt0) cc_final: 0.7173 (tt0) REVERT: I 1119 MET cc_start: 0.8366 (tpp) cc_final: 0.7982 (tpp) REVERT: I 1204 LEU cc_start: 0.9188 (mt) cc_final: 0.8610 (mt) REVERT: I 1274 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7785 (mm-30) REVERT: I 1279 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8014 (mt-10) REVERT: J 133 ARG cc_start: 0.8504 (mmm-85) cc_final: 0.8136 (mmt90) REVERT: J 169 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7781 (tt) REVERT: J 180 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.6694 (tmt) REVERT: J 382 TYR cc_start: 0.9034 (m-10) cc_final: 0.8809 (m-10) REVERT: J 697 MET cc_start: 0.6636 (tmm) cc_final: 0.6233 (tmm) REVERT: J 788 LEU cc_start: 0.9290 (mm) cc_final: 0.8644 (tt) REVERT: J 806 ASP cc_start: 0.7463 (p0) cc_final: 0.6788 (p0) REVERT: J 822 MET cc_start: 0.8246 (tpp) cc_final: 0.7953 (tpt) REVERT: J 902 ASP cc_start: 0.8173 (t70) cc_final: 0.7869 (t70) REVERT: J 925 GLU cc_start: 0.8598 (pp20) cc_final: 0.8334 (pp20) REVERT: J 1030 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: J 1254 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7725 (mt-10) REVERT: J 1260 MET cc_start: 0.8653 (mtt) cc_final: 0.8414 (mtt) REVERT: K 8 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8088 (p0) REVERT: K 31 GLN cc_start: 0.8175 (tt0) cc_final: 0.7875 (tt0) REVERT: K 60 ASN cc_start: 0.7927 (p0) cc_final: 0.7691 (p0) REVERT: K 75 GLN cc_start: 0.8550 (pp30) cc_final: 0.8211 (pp30) outliers start: 71 outliers final: 58 residues processed: 380 average time/residue: 0.1602 time to fit residues: 102.2064 Evaluate side-chains 385 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 319 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 459 MET Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1274 GLU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1299 ASN Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 710 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1030 GLU Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1248 ILE Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 55 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 266 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 201 optimal weight: 0.1980 chunk 117 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 ASN ** 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 = 0.3555 r_free = 0.3555 target = 0.124732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.099692 restraints weight = 50029.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.099053 restraints weight = 32989.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.099822 restraints weight = 27078.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.100225 restraints weight = 23314.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.100322 restraints weight = 21721.611| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 26764 Z= 0.213 Angle : 0.687 15.571 36432 Z= 0.347 Chirality : 0.045 0.271 4176 Planarity : 0.004 0.087 4541 Dihedral : 13.799 175.380 4198 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.85 % Allowed : 19.47 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -1.29 (0.15), residues: 3174 helix: 0.66 (0.16), residues: 1123 sheet: -1.54 (0.26), residues: 382 loop : -1.80 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 69 TYR 0.014 0.001 TYR J 772 PHE 0.025 0.001 PHE I1025 TRP 0.009 0.001 TRP J1193 HIS 0.007 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (26756) covalent geometry : angle 0.68581 / 0.35 (36420) hydrogen bonds : bond 0.03913 / 4.42 ( 1030) hydrogen bonds : angle 4.71584 / 5.00 ( 2818) metal coordination : bond 0.01096 / 0.99 ( 8) metal coordination : angle 1.84369 / 3.61 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3537.00 seconds wall clock time: 62 minutes 8.32 seconds (3728.32 seconds total)