Starting phenix.real_space_refine on Mon Aug 25 08:49:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eh9_28144/08_2025/8eh9_28144.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eh9_28144/08_2025/8eh9_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 { model { file = "/net/cci-nas-00/data/ceres_data/8eh9_28144/08_2025/8eh9_28144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eh9_28144/08_2025/8eh9_28144.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eh9_28144/08_2025/8eh9_28144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eh9_28144/08_2025/8eh9_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: {'RNA': 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: 13 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: 5.84, per 1000 atoms: 0.22 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: 1.99 Conformation dependent library (CDL) restraints added in 808.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.77 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: 5.61 Time building geometry restraints manager: 2.72 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: 35995 2.77 - 5.55: 367 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=" 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=" C PRO I 43 " pdb=" N GLU I 44 " pdb=" CA GLU I 44 " ideal model delta sigma weight residual 122.61 129.30 -6.69 1.56e+00 4.11e-01 1.84e+01 angle pdb=" C VAL J 518 " pdb=" N ASN J 519 " pdb=" CA ASN J 519 " ideal model delta sigma weight residual 122.19 131.77 -9.58 2.30e+00 1.89e-01 1.74e+01 angle pdb=" C MET I1290 " pdb=" N LEU I1291 " pdb=" CA LEU I1291 " ideal model delta sigma weight residual 122.08 115.63 6.45 1.59e+00 3.96e-01 1.64e+01 ... (remaining 36415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 15835 35.79 - 71.58: 514 71.58 - 107.37: 41 107.37 - 143.16: 1 143.16 - 178.95: 1 Dihedral angle restraints: 16392 sinusoidal: 7241 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=" CA VAL I1309 " pdb=" C VAL I1309 " pdb=" N ASP I1310 " pdb=" CA ASP I1310 " ideal model delta harmonic sigma weight residual 180.00 151.55 28.45 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 16389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3822 0.083 - 0.166: 341 0.166 - 0.248: 10 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.250 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.295 26764 Z= 0.220 Angle : 0.747 13.865 36432 Z= 0.407 Chirality : 0.046 0.414 4176 Planarity : 0.005 0.092 4541 Dihedral : 16.723 178.948 10508 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 aren 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 covalent geometry : bond 0.00447 (26756) covalent geometry : angle 0.74614 (36420) hydrogen bonds : bond 0.18486 ( 1030) hydrogen bonds : angle 6.84255 ( 2818) metal coordination : bond 0.00377 ( 8) metal coordination : angle 2.46938 ( 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 : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 41 ASN cc_start: 0.8079 (t0) cc_final: 0.7417 (t0) REVERT: I 68 LEU cc_start: 0.8206 (tp) cc_final: 0.7983 (tt) REVERT: I 85 CYS cc_start: 0.8611 (m) cc_final: 0.8396 (m) REVERT: I 427 ASP cc_start: 0.7839 (m-30) cc_final: 0.7374 (m-30) REVERT: I 468 LEU cc_start: 0.8810 (tp) cc_final: 0.8370 (tp) REVERT: I 834 GLN cc_start: 0.8084 (pt0) cc_final: 0.7759 (pt0) REVERT: I 1248 THR cc_start: 0.8034 (t) cc_final: 0.7634 (t) REVERT: J 151 MET cc_start: 0.7165 (mpp) cc_final: 0.6710 (ppp) REVERT: J 382 TYR cc_start: 0.9024 (m-10) cc_final: 0.8778 (m-10) REVERT: J 679 TYR cc_start: 0.6983 (t80) cc_final: 0.6770 (t80) REVERT: J 697 MET cc_start: 0.6775 (tmm) cc_final: 0.6263 (tmm) REVERT: J 806 ASP cc_start: 0.7524 (p0) cc_final: 0.6726 (p0) REVERT: J 1258 ARG cc_start: 0.8116 (ttt90) cc_final: 0.7604 (ttt90) REVERT: K 68 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8256 (mm-30) outliers start: 1 outliers final: 0 residues processed: 475 average time/residue: 0.1411 time to fit residues: 108.9249 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 : 0.758 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.127679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.102825 restraints weight = 50360.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.102054 restraints weight = 32814.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.102665 restraints weight = 29040.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.103284 restraints weight = 24136.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.103309 restraints weight = 21671.589| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26764 Z= 0.187 Angle : 0.642 10.804 36432 Z= 0.333 Chirality : 0.044 0.230 4176 Planarity : 0.005 0.091 4541 Dihedral : 14.486 177.115 4311 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.30 % Allowed : 11.11 % Favored : 87.60 % 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 aren not related in a simple way. whole: -1.57 (0.14), residues: 3174 helix: 0.44 (0.16), residues: 1105 sheet: -1.93 (0.27), residues: 372 loop : -1.89 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 211 TYR 0.012 0.001 TYR J 723 PHE 0.021 0.001 PHE I 337 TRP 0.013 0.001 TRP J 115 HIS 0.007 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00431 (26756) covalent geometry : angle 0.64049 (36420) hydrogen bonds : bond 0.04327 ( 1030) hydrogen bonds : angle 5.16610 ( 2818) metal coordination : bond 0.00918 ( 8) metal coordination : angle 2.69870 ( 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 409 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 374 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8025 (ptmt) REVERT: H 185 TYR cc_start: 0.8974 (p90) cc_final: 0.8630 (p90) REVERT: H 206 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6732 (tm-30) REVERT: I 68 LEU cc_start: 0.8460 (tp) cc_final: 0.8209 (tp) REVERT: I 85 CYS cc_start: 0.8903 (m) cc_final: 0.8597 (m) REVERT: I 108 GLU cc_start: 0.5656 (mm-30) cc_final: 0.5430 (mm-30) REVERT: I 311 CYS cc_start: 0.6580 (p) cc_final: 0.6291 (p) REVERT: I 472 GLU cc_start: 0.8403 (tp30) cc_final: 0.7858 (tp30) REVERT: I 527 LYS cc_start: 0.9355 (mttt) cc_final: 0.9018 (mtmm) REVERT: I 728 ASP cc_start: 0.7814 (t0) cc_final: 0.7469 (t0) REVERT: I 930 ASP cc_start: 0.8363 (t70) cc_final: 0.8112 (t0) REVERT: I 1329 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7419 (mt-10) REVERT: J 133 ARG cc_start: 0.8538 (mmm-85) cc_final: 0.7919 (mmt90) REVERT: J 382 TYR cc_start: 0.9151 (m-10) cc_final: 0.8871 (m-10) REVERT: J 403 ARG cc_start: 0.7579 (mtp-110) cc_final: 0.7154 (tmm-80) REVERT: J 466 MET cc_start: 0.8573 (mtm) cc_final: 0.8334 (mtm) REVERT: J 697 MET cc_start: 0.6439 (tmm) cc_final: 0.5943 (tmm) REVERT: J 788 LEU cc_start: 0.9240 (mm) cc_final: 0.8753 (tt) REVERT: J 806 ASP cc_start: 0.7495 (p0) cc_final: 0.6743 (p0) REVERT: J 807 LEU cc_start: 0.9158 (tt) cc_final: 0.8941 (tt) REVERT: J 1236 GLU cc_start: 0.6328 (tp30) cc_final: 0.5997 (tp30) REVERT: J 1254 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7717 (mt-10) REVERT: K 60 ASN cc_start: 0.7672 (p0) cc_final: 0.7458 (p0) outliers start: 35 outliers final: 21 residues processed: 397 average time/residue: 0.1686 time to fit residues: 107.8533 Evaluate side-chains 358 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 337 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 135 THR 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 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 587 LEU Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1090 ILE Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1257 VAL 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: 4.9990 chunk 34 optimal weight: 1.9990 chunk 273 optimal weight: 0.6980 chunk 17 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 294 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 165 HIS I 276 GLN I 554 HIS ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 922 ASN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1049 GLN J1126 GLN J1326 GLN J1366 HIS K 15 ASN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.124706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.099105 restraints weight = 50569.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.099175 restraints weight = 34343.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.099998 restraints weight = 28464.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.100410 restraints weight = 23469.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.100473 restraints weight = 21568.531| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 26764 Z= 0.238 Angle : 0.660 12.160 36432 Z= 0.342 Chirality : 0.044 0.165 4176 Planarity : 0.005 0.093 4541 Dihedral : 14.268 176.619 4311 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.52 % Allowed : 14.03 % Favored : 83.45 % 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 aren not related in a simple way. whole: -1.53 (0.15), residues: 3174 helix: 0.50 (0.16), residues: 1095 sheet: -1.88 (0.26), residues: 379 loop : -1.88 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 60 TYR 0.015 0.002 TYR J 772 PHE 0.013 0.002 PHE J 437 TRP 0.010 0.001 TRP J 115 HIS 0.011 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00551 (26756) covalent geometry : angle 0.65866 (36420) hydrogen bonds : bond 0.04224 ( 1030) hydrogen bonds : angle 4.98783 ( 2818) metal coordination : bond 0.01271 ( 8) metal coordination : angle 2.66454 ( 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 412 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 344 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8487 (ttmt) cc_final: 0.7949 (ptmt) REVERT: I 85 CYS cc_start: 0.9020 (m) cc_final: 0.8693 (m) REVERT: I 108 GLU cc_start: 0.5649 (mm-30) cc_final: 0.5438 (mm-30) REVERT: I 274 ILE cc_start: 0.6832 (OUTLIER) cc_final: 0.6500 (tt) REVERT: I 527 LYS cc_start: 0.9367 (mttt) cc_final: 0.9063 (mtmm) REVERT: I 728 ASP cc_start: 0.7656 (t0) cc_final: 0.7194 (t0) REVERT: I 1274 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7942 (mm-30) REVERT: I 1329 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7529 (mt-10) REVERT: J 133 ARG cc_start: 0.8516 (mmm-85) cc_final: 0.8080 (mmt90) REVERT: J 382 TYR cc_start: 0.9146 (m-10) cc_final: 0.8877 (m-10) REVERT: J 697 MET cc_start: 0.6495 (tmm) cc_final: 0.6065 (tmm) REVERT: J 788 LEU cc_start: 0.9100 (mm) cc_final: 0.8645 (tt) REVERT: J 806 ASP cc_start: 0.7607 (p0) cc_final: 0.6910 (p0) REVERT: J 807 LEU cc_start: 0.9239 (tt) cc_final: 0.9005 (tt) REVERT: J 1040 MET cc_start: 0.6277 (ptp) cc_final: 0.6011 (mtm) REVERT: J 1152 GLU cc_start: 0.7616 (mp0) cc_final: 0.7257 (mp0) REVERT: J 1254 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7823 (mt-10) REVERT: K 8 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8558 (p0) REVERT: K 65 ASP cc_start: 0.8680 (p0) cc_final: 0.8457 (p0) outliers start: 68 outliers final: 47 residues processed: 388 average time/residue: 0.1587 time to fit residues: 101.1746 Evaluate side-chains 359 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 309 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU 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 39 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 491 ASP Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 765 ILE 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 1332 SER Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 298 MET Chi-restraints excluded: chain J residue 316 ILE 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 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 1090 ILE Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1257 VAL 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 15 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 257 optimal weight: 2.9990 chunk 6 optimal weight: 0.0040 chunk 223 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 195 optimal weight: 20.0000 chunk 303 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 143 optimal weight: 0.0000 chunk 315 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN I 165 HIS I 276 GLN ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 922 ASN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1049 GLN K 31 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.129644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.103813 restraints weight = 49533.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.104692 restraints weight = 30112.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.105385 restraints weight = 22987.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.106003 restraints weight = 20470.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105938 restraints weight = 18372.008| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26764 Z= 0.112 Angle : 0.580 13.232 36432 Z= 0.299 Chirality : 0.041 0.153 4176 Planarity : 0.004 0.090 4541 Dihedral : 14.132 177.146 4311 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.96 % Allowed : 16.77 % Favored : 81.27 % 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 aren not related in a simple way. whole: -1.19 (0.15), residues: 3174 helix: 0.82 (0.16), residues: 1099 sheet: -1.63 (0.28), residues: 357 loop : -1.74 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 16 TYR 0.017 0.001 TYR J 165 PHE 0.025 0.001 PHE I 337 TRP 0.008 0.001 TRP J 115 HIS 0.024 0.001 HIS J1366 Details of bonding type rmsd covalent geometry : bond 0.00249 (26756) covalent geometry : angle 0.57876 (36420) hydrogen bonds : bond 0.03560 ( 1030) hydrogen bonds : angle 4.58476 ( 2818) metal coordination : bond 0.00340 ( 8) metal coordination : angle 2.02491 ( 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 434 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 381 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8529 (ttmt) cc_final: 0.8021 (ptmt) REVERT: H 185 TYR cc_start: 0.9204 (p90) cc_final: 0.8853 (p90) REVERT: H 206 GLU cc_start: 0.7031 (tm-30) cc_final: 0.5774 (tm-30) REVERT: I 85 CYS cc_start: 0.8872 (m) cc_final: 0.8514 (m) REVERT: I 108 GLU cc_start: 0.5593 (mm-30) cc_final: 0.5379 (mm-30) REVERT: I 274 ILE cc_start: 0.6879 (OUTLIER) cc_final: 0.6536 (tt) REVERT: I 527 LYS cc_start: 0.9249 (mttt) cc_final: 0.9020 (mtmm) REVERT: I 728 ASP cc_start: 0.7645 (t0) cc_final: 0.7210 (t0) REVERT: I 834 GLN cc_start: 0.8088 (pt0) cc_final: 0.7793 (pt0) REVERT: I 1119 MET cc_start: 0.8524 (tpp) cc_final: 0.8321 (tpp) REVERT: I 1204 LEU cc_start: 0.8933 (mt) cc_final: 0.8071 (mt) REVERT: I 1279 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8133 (mt-10) REVERT: J 133 ARG cc_start: 0.8546 (mmm-85) cc_final: 0.8087 (mmt90) REVERT: J 136 GLU cc_start: 0.8396 (pp20) cc_final: 0.7906 (pp20) REVERT: J 169 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7826 (tt) REVERT: J 180 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.6472 (tmt) REVERT: J 382 TYR cc_start: 0.9007 (m-10) cc_final: 0.8668 (m-10) REVERT: J 466 MET cc_start: 0.8312 (mtp) cc_final: 0.7915 (mtm) REVERT: J 697 MET cc_start: 0.6475 (tmm) cc_final: 0.6043 (tmm) REVERT: J 788 LEU cc_start: 0.9092 (mm) cc_final: 0.8558 (tt) REVERT: J 806 ASP cc_start: 0.7484 (p0) cc_final: 0.6836 (p0) REVERT: J 807 LEU cc_start: 0.9149 (tt) cc_final: 0.8927 (tt) REVERT: J 1152 GLU cc_start: 0.7505 (mp0) cc_final: 0.7136 (mp0) REVERT: K 8 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8145 (p0) REVERT: K 60 ASN cc_start: 0.7916 (p0) cc_final: 0.7393 (p0) REVERT: K 71 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8541 (tm-30) outliers start: 53 outliers final: 30 residues processed: 415 average time/residue: 0.1548 time to fit residues: 106.0707 Evaluate side-chains 370 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 336 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU 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 194 LEU Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 420 LEU 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 1222 GLU Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 553 THR 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 1041 ILE Chi-restraints excluded: chain J residue 1049 GLN Chi-restraints excluded: chain J residue 1090 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 199 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 262 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 291 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 316 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 147 GLN I 165 HIS ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1049 GLN ** K 75 GLN ** 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 = 0.3606 r_free = 0.3606 target = 0.128511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.103109 restraints weight = 49853.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.103553 restraints weight = 32834.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.104098 restraints weight = 26590.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104668 restraints weight = 22333.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.104766 restraints weight = 19726.338| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26764 Z= 0.137 Angle : 0.589 13.908 36432 Z= 0.302 Chirality : 0.042 0.229 4176 Planarity : 0.004 0.088 4541 Dihedral : 14.047 175.884 4311 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.63 % Allowed : 17.51 % Favored : 79.86 % 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 aren not related in a simple way. whole: -1.12 (0.15), residues: 3174 helix: 0.84 (0.16), residues: 1108 sheet: -1.53 (0.27), residues: 370 loop : -1.70 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 69 TYR 0.014 0.001 TYR J 165 PHE 0.018 0.001 PHE J 668 TRP 0.014 0.001 TRP J 236 HIS 0.009 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00315 (26756) covalent geometry : angle 0.58844 (36420) hydrogen bonds : bond 0.03557 ( 1030) hydrogen bonds : angle 4.50820 ( 2818) metal coordination : bond 0.00684 ( 8) metal coordination : angle 1.67911 ( 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 432 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 361 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8592 (ttmt) cc_final: 0.8133 (ptmt) REVERT: H 147 GLN cc_start: 0.8266 (mt0) cc_final: 0.7939 (mm110) REVERT: H 185 TYR cc_start: 0.9167 (p90) cc_final: 0.8852 (p90) REVERT: H 206 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6022 (tm-30) REVERT: I 85 CYS cc_start: 0.8898 (m) cc_final: 0.8509 (m) REVERT: I 274 ILE cc_start: 0.6719 (OUTLIER) cc_final: 0.6361 (tt) REVERT: I 369 MET cc_start: 0.7357 (tmm) cc_final: 0.6919 (ppp) REVERT: I 427 ASP cc_start: 0.8340 (m-30) cc_final: 0.7778 (m-30) REVERT: I 472 GLU cc_start: 0.8188 (tp30) cc_final: 0.7857 (tp30) REVERT: I 527 LYS cc_start: 0.9236 (mttt) cc_final: 0.9020 (mtmm) REVERT: I 728 ASP cc_start: 0.7639 (t0) cc_final: 0.7344 (t0) REVERT: I 834 GLN cc_start: 0.8095 (pt0) cc_final: 0.7819 (pt0) REVERT: I 1204 LEU cc_start: 0.9071 (mt) cc_final: 0.8142 (mt) REVERT: I 1231 TYR cc_start: 0.9127 (OUTLIER) cc_final: 0.8645 (t80) REVERT: I 1274 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7874 (mm-30) REVERT: I 1279 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7996 (mt-10) REVERT: J 133 ARG cc_start: 0.8572 (mmm-85) cc_final: 0.8108 (mmt90) REVERT: J 136 GLU cc_start: 0.8302 (pp20) cc_final: 0.7869 (pp20) REVERT: J 169 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7720 (tt) REVERT: J 180 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6407 (tmt) REVERT: J 382 TYR cc_start: 0.9020 (m-10) cc_final: 0.8784 (m-10) REVERT: J 697 MET cc_start: 0.6699 (tmm) cc_final: 0.6313 (tmm) REVERT: J 788 LEU cc_start: 0.9135 (mm) cc_final: 0.8557 (tt) REVERT: J 806 ASP cc_start: 0.7394 (p0) cc_final: 0.6723 (p0) REVERT: J 1030 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: K 8 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8158 (p0) REVERT: K 60 ASN cc_start: 0.8048 (p0) cc_final: 0.7634 (p0) REVERT: K 71 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8555 (tm-30) outliers start: 71 outliers final: 49 residues processed: 405 average time/residue: 0.1437 time to fit residues: 96.8146 Evaluate side-chains 387 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 331 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 SER 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 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 135 THR Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 442 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 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 1231 TYR 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 J residue 48 THR Chi-restraints excluded: chain J residue 130 MET 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 442 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 573 THR 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 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 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 K residue 8 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 170 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 281 optimal weight: 9.9990 chunk 95 optimal weight: 0.5980 chunk 298 optimal weight: 10.0000 chunk 224 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 234 optimal weight: 8.9990 chunk 284 optimal weight: 8.9990 chunk 156 optimal weight: 0.5980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 165 HIS ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 688 GLN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1049 GLN K 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.101393 restraints weight = 49990.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.101227 restraints weight = 31562.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.101804 restraints weight = 27160.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.102407 restraints weight = 23548.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102496 restraints weight = 20643.680| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2193 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= 0.182 Angle : 0.618 14.334 36432 Z= 0.318 Chirality : 0.043 0.187 4176 Planarity : 0.004 0.093 4541 Dihedral : 14.054 175.282 4311 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.81 % Allowed : 18.55 % Favored : 78.64 % 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 aren not related in a simple way. whole: -1.16 (0.15), residues: 3174 helix: 0.79 (0.16), residues: 1112 sheet: -1.52 (0.27), residues: 377 loop : -1.72 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J1048 TYR 0.013 0.001 TYR G 152 PHE 0.018 0.001 PHE I 828 TRP 0.007 0.001 TRP J1193 HIS 0.019 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00422 (26756) covalent geometry : angle 0.61743 (36420) hydrogen bonds : bond 0.03690 ( 1030) hydrogen bonds : angle 4.54681 ( 2818) metal coordination : bond 0.00931 ( 8) metal coordination : angle 1.58495 ( 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 418 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 342 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8606 (ttmt) cc_final: 0.8144 (ptmt) REVERT: H 185 TYR cc_start: 0.9349 (p90) cc_final: 0.9071 (p90) REVERT: I 85 CYS cc_start: 0.9003 (m) cc_final: 0.8606 (m) REVERT: I 274 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6519 (tt) REVERT: I 459 MET cc_start: 0.8947 (mpp) cc_final: 0.8743 (mpp) REVERT: I 472 GLU cc_start: 0.8352 (tp30) cc_final: 0.7947 (tp30) REVERT: I 527 LYS cc_start: 0.9289 (mttt) cc_final: 0.9041 (mtmm) REVERT: I 704 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6707 (ttm) REVERT: I 728 ASP cc_start: 0.7652 (t0) cc_final: 0.7319 (t0) REVERT: I 1119 MET cc_start: 0.8530 (tpp) cc_final: 0.8131 (tpp) REVERT: I 1204 LEU cc_start: 0.9072 (mt) cc_final: 0.8568 (mt) REVERT: I 1231 TYR cc_start: 0.9198 (OUTLIER) cc_final: 0.8671 (t80) REVERT: I 1274 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7909 (mm-30) REVERT: I 1279 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8109 (mt-10) REVERT: J 133 ARG cc_start: 0.8649 (mmm-85) cc_final: 0.7941 (mmt90) REVERT: J 169 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7808 (tt) REVERT: J 180 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.6526 (tmt) REVERT: J 382 TYR cc_start: 0.9047 (m-10) cc_final: 0.8813 (m-10) REVERT: J 697 MET cc_start: 0.6551 (tmm) cc_final: 0.6210 (tmm) REVERT: J 788 LEU cc_start: 0.9141 (mm) cc_final: 0.8586 (tt) REVERT: J 806 ASP cc_start: 0.7509 (p0) cc_final: 0.6868 (p0) REVERT: J 822 MET cc_start: 0.8260 (tpp) cc_final: 0.8026 (tpt) REVERT: J 902 ASP cc_start: 0.8096 (t70) cc_final: 0.7823 (t70) REVERT: J 1030 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: J 1260 MET cc_start: 0.8794 (mtt) cc_final: 0.8516 (mtt) REVERT: K 8 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8369 (p0) REVERT: K 55 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8124 (pt0) REVERT: K 60 ASN cc_start: 0.8008 (p0) cc_final: 0.7725 (p0) REVERT: K 62 GLN cc_start: 0.8413 (tp40) cc_final: 0.7998 (tp40) outliers start: 76 outliers final: 53 residues processed: 391 average time/residue: 0.1416 time to fit residues: 90.8985 Evaluate side-chains 380 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 318 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 131 CYS 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 135 THR Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 315 MET 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 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 1231 TYR 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 J residue 48 THR 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 415 VAL 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 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 862 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1002 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 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: 0.9980 chunk 1 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 437 ASN ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 688 GLN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1049 GLN ** K 75 GLN ** 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 = 0.3599 r_free = 0.3599 target = 0.128097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.102339 restraints weight = 49495.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.102899 restraints weight = 30927.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.103508 restraints weight = 23817.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.104204 restraints weight = 20892.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.104288 restraints weight = 18867.765| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26764 Z= 0.126 Angle : 0.593 15.265 36432 Z= 0.303 Chirality : 0.042 0.229 4176 Planarity : 0.004 0.090 4541 Dihedral : 14.035 175.485 4311 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.67 % Allowed : 19.62 % Favored : 77.71 % 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 aren not related in a simple way. whole: -1.01 (0.15), residues: 3174 helix: 0.92 (0.16), residues: 1107 sheet: -1.39 (0.27), residues: 375 loop : -1.64 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 407 TYR 0.020 0.001 TYR G 152 PHE 0.020 0.001 PHE J 620 TRP 0.010 0.001 TRP J 236 HIS 0.005 0.001 HIS G 23 Details of bonding type rmsd covalent geometry : bond 0.00291 (26756) covalent geometry : angle 0.59277 (36420) hydrogen bonds : bond 0.03442 ( 1030) hydrogen bonds : angle 4.41513 ( 2818) metal coordination : bond 0.00450 ( 8) metal coordination : angle 1.51025 ( 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 430 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 358 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 200 LYS cc_start: 0.8636 (ttmt) cc_final: 0.8200 (ptmt) REVERT: H 147 GLN cc_start: 0.8456 (mt0) cc_final: 0.8143 (mm110) REVERT: H 185 TYR cc_start: 0.9312 (p90) cc_final: 0.9095 (p90) REVERT: I 85 CYS cc_start: 0.8866 (m) cc_final: 0.8464 (m) REVERT: I 274 ILE cc_start: 0.6834 (OUTLIER) cc_final: 0.6487 (tt) REVERT: I 369 MET cc_start: 0.7392 (tmm) cc_final: 0.7157 (ppp) REVERT: I 427 ASP cc_start: 0.8344 (m-30) cc_final: 0.7755 (m-30) REVERT: I 459 MET cc_start: 0.8935 (mpp) cc_final: 0.8629 (mpp) REVERT: I 472 GLU cc_start: 0.8264 (tp30) cc_final: 0.7889 (tp30) REVERT: I 704 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6655 (ttm) REVERT: I 705 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7562 (mt-10) REVERT: I 731 ARG cc_start: 0.8325 (ptm160) cc_final: 0.8087 (ptp90) REVERT: I 1119 MET cc_start: 0.8441 (tpp) cc_final: 0.8184 (tpp) REVERT: I 1204 LEU cc_start: 0.9134 (mt) cc_final: 0.8366 (mt) REVERT: I 1231 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.8730 (t80) REVERT: I 1279 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7985 (mt-10) REVERT: J 133 ARG cc_start: 0.8527 (mmm-85) cc_final: 0.8146 (mmt90) REVERT: J 169 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7747 (tt) REVERT: J 180 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.6464 (tmt) REVERT: J 236 TRP cc_start: 0.8536 (m-10) cc_final: 0.8088 (m-90) REVERT: J 264 ASP cc_start: 0.7569 (m-30) cc_final: 0.7266 (t0) REVERT: J 382 TYR cc_start: 0.8977 (m-10) cc_final: 0.8755 (m-10) REVERT: J 697 MET cc_start: 0.6534 (tmm) cc_final: 0.6218 (tmm) REVERT: J 788 LEU cc_start: 0.9146 (mm) cc_final: 0.8582 (tt) REVERT: J 806 ASP cc_start: 0.7470 (p0) cc_final: 0.6756 (p0) REVERT: J 822 MET cc_start: 0.8209 (tpp) cc_final: 0.7976 (tpt) REVERT: J 902 ASP cc_start: 0.8055 (t70) cc_final: 0.7855 (t70) REVERT: J 1030 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: J 1151 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7967 (tptp) REVERT: J 1260 MET cc_start: 0.8806 (mtt) cc_final: 0.8559 (mtt) REVERT: K 8 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8333 (p0) REVERT: K 31 GLN cc_start: 0.7994 (tt0) cc_final: 0.7701 (tt0) REVERT: K 55 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8094 (pt0) outliers start: 72 outliers final: 46 residues processed: 408 average time/residue: 0.1658 time to fit residues: 111.1125 Evaluate side-chains 384 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 329 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 131 CYS 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 11 ILE 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 448 LEU 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 1176 LEU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1231 TYR 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 J residue 48 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 668 PHE 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 862 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 918 ILE 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 1151 LYS Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1184 ASP 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: 6.9990 chunk 75 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 295 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 209 optimal weight: 0.7980 chunk 180 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN I 120 GLN ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1049 GLN K 73 GLN ** 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 = 0.3546 r_free = 0.3546 target = 0.124215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.098779 restraints weight = 50292.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.098591 restraints weight = 31826.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.099084 restraints weight = 26617.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.099553 restraints weight = 24262.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099725 restraints weight = 21613.035| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 26764 Z= 0.241 Angle : 0.686 13.601 36432 Z= 0.350 Chirality : 0.044 0.222 4176 Planarity : 0.005 0.092 4541 Dihedral : 14.162 174.613 4311 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.81 % Allowed : 20.03 % Favored : 77.16 % 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 aren not related in a simple way. whole: -1.22 (0.15), residues: 3174 helix: 0.72 (0.16), residues: 1111 sheet: -1.54 (0.26), residues: 383 loop : -1.73 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 69 TYR 0.022 0.002 TYR G 152 PHE 0.021 0.002 PHE I 828 TRP 0.010 0.001 TRP J1193 HIS 0.005 0.001 HIS J 651 Details of bonding type rmsd covalent geometry : bond 0.00558 (26756) covalent geometry : angle 0.68491 (36420) hydrogen bonds : bond 0.03936 ( 1030) hydrogen bonds : angle 4.67630 ( 2818) metal coordination : bond 0.01212 ( 8) metal coordination : angle 1.83471 ( 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 410 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 334 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 HIS cc_start: 0.8153 (OUTLIER) cc_final: 0.7137 (p-80) REVERT: G 200 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8207 (ptmt) REVERT: G 205 MET cc_start: 0.8928 (ptp) cc_final: 0.8661 (ttp) REVERT: H 147 GLN cc_start: 0.8409 (mt0) cc_final: 0.8117 (mm110) REVERT: I 85 CYS cc_start: 0.8942 (m) cc_final: 0.8586 (m) REVERT: I 274 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6719 (tt) REVERT: I 472 GLU cc_start: 0.8312 (tp30) cc_final: 0.7931 (tp30) REVERT: I 704 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.6956 (ttm) REVERT: I 728 ASP cc_start: 0.7827 (t0) cc_final: 0.7553 (t0) REVERT: I 814 ASP cc_start: 0.8586 (m-30) cc_final: 0.8382 (m-30) REVERT: I 1231 TYR cc_start: 0.9165 (OUTLIER) cc_final: 0.8752 (t80) REVERT: I 1274 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7880 (mm-30) REVERT: I 1279 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8085 (mt-10) REVERT: J 133 ARG cc_start: 0.8597 (mmm-85) cc_final: 0.8231 (mmt90) REVERT: J 165 TYR cc_start: 0.8653 (t80) cc_final: 0.8414 (t80) REVERT: J 169 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7899 (tt) REVERT: J 180 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.6732 (tmt) REVERT: J 236 TRP cc_start: 0.8721 (m-10) cc_final: 0.8294 (m-90) REVERT: J 788 LEU cc_start: 0.9203 (mm) cc_final: 0.8709 (tt) REVERT: J 806 ASP cc_start: 0.7514 (p0) cc_final: 0.6842 (p0) REVERT: J 1030 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: J 1236 GLU cc_start: 0.6884 (tp30) cc_final: 0.6668 (tp30) REVERT: J 1254 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7809 (mt-10) REVERT: J 1260 MET cc_start: 0.8811 (mtt) cc_final: 0.8600 (mtt) REVERT: K 8 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8423 (p0) REVERT: K 55 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8094 (pt0) REVERT: K 60 ASN cc_start: 0.8367 (p0) cc_final: 0.8032 (p0) REVERT: K 62 GLN cc_start: 0.8294 (tp40) cc_final: 0.8074 (tp40) outliers start: 76 outliers final: 58 residues processed: 382 average time/residue: 0.1468 time to fit residues: 93.8707 Evaluate side-chains 392 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 324 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 131 CYS 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 11 ILE Chi-restraints excluded: chain I residue 39 ILE 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 442 VAL 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 1231 TYR 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 J residue 48 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 176 PHE 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 434 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 668 PHE 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 808 VAL Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1002 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 113 optimal weight: 0.5980 chunk 287 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 chunk 28 optimal weight: 0.0060 chunk 186 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 252 optimal weight: 0.4980 chunk 297 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN I 150 HIS ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1049 GLN K 73 GLN ** 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 = 0.3603 r_free = 0.3603 target = 0.128370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102776 restraints weight = 49468.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103336 restraints weight = 30749.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.104179 restraints weight = 23945.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.104635 restraints weight = 20053.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104715 restraints weight = 18731.213| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26764 Z= 0.117 Angle : 0.618 16.380 36432 Z= 0.311 Chirality : 0.042 0.230 4176 Planarity : 0.004 0.088 4541 Dihedral : 14.079 175.384 4311 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.67 % Allowed : 20.84 % Favored : 76.49 % 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 aren not related in a simple way. whole: -0.98 (0.15), residues: 3174 helix: 0.96 (0.16), residues: 1099 sheet: -1.35 (0.27), residues: 372 loop : -1.62 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 407 TYR 0.018 0.001 TYR G 152 PHE 0.017 0.001 PHE I 828 TRP 0.013 0.001 TRP J 236 HIS 0.007 0.001 HIS J 450 Details of bonding type rmsd covalent geometry : bond 0.00267 (26756) covalent geometry : angle 0.61722 (36420) hydrogen bonds : bond 0.03428 ( 1030) hydrogen bonds : angle 4.40924 ( 2818) metal coordination : bond 0.00276 ( 8) metal coordination : angle 1.39238 ( 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 432 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 360 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 HIS cc_start: 0.7988 (OUTLIER) cc_final: 0.6883 (p-80) REVERT: G 200 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8293 (ptmt) REVERT: I 85 CYS cc_start: 0.8829 (m) cc_final: 0.8439 (m) REVERT: I 274 ILE cc_start: 0.6896 (OUTLIER) cc_final: 0.6553 (tt) REVERT: I 427 ASP cc_start: 0.8322 (m-30) cc_final: 0.7740 (m-30) REVERT: I 472 GLU cc_start: 0.8208 (tp30) cc_final: 0.7834 (tp30) REVERT: I 504 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7729 (tm-30) REVERT: I 705 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7646 (mt-10) REVERT: I 731 ARG cc_start: 0.8315 (ptm160) cc_final: 0.8091 (ptp90) REVERT: I 1214 ASP cc_start: 0.9192 (t0) cc_final: 0.8896 (t0) REVERT: I 1231 TYR cc_start: 0.9095 (OUTLIER) cc_final: 0.8773 (t80) REVERT: I 1274 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7705 (mm-30) REVERT: I 1279 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8035 (mt-10) REVERT: I 1291 LEU cc_start: 0.8827 (pp) cc_final: 0.8479 (pt) REVERT: J 133 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8219 (mmt90) REVERT: J 165 TYR cc_start: 0.8693 (t80) cc_final: 0.8139 (t80) REVERT: J 169 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7912 (tt) REVERT: J 180 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.6489 (tmt) REVERT: J 236 TRP cc_start: 0.8302 (m-10) cc_final: 0.7910 (m-90) REVERT: J 264 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.6844 (t0) REVERT: J 382 TYR cc_start: 0.9004 (m-10) cc_final: 0.8593 (m-10) REVERT: J 788 LEU cc_start: 0.9145 (mm) cc_final: 0.8581 (tt) REVERT: J 806 ASP cc_start: 0.7363 (p0) cc_final: 0.6730 (p0) REVERT: J 1030 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: K 55 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8070 (pt0) REVERT: K 60 ASN cc_start: 0.8153 (p0) cc_final: 0.7748 (p0) outliers start: 72 outliers final: 50 residues processed: 406 average time/residue: 0.1578 time to fit residues: 105.9741 Evaluate side-chains 391 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 332 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 131 CYS 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 11 ILE 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 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 1222 GLU Chi-restraints excluded: chain I residue 1231 TYR 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 J residue 48 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 474 LEU Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 573 THR 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 668 PHE 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 862 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1002 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 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: 2.9990 chunk 68 optimal weight: 0.9980 chunk 193 optimal weight: 9.9990 chunk 61 optimal weight: 0.0570 chunk 160 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 290 optimal weight: 0.0670 chunk 149 optimal weight: 0.6980 chunk 129 optimal weight: 0.1980 chunk 212 optimal weight: 0.6980 chunk 295 optimal weight: 0.2980 overall best weight: 0.2636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 120 GLN ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1049 GLN K 31 GLN ** 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 = 0.3647 r_free = 0.3647 target = 0.131462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105844 restraints weight = 49511.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106584 restraints weight = 31322.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.106945 restraints weight = 25010.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.107573 restraints weight = 22599.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.107636 restraints weight = 20364.388| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26764 Z= 0.114 Angle : 0.618 16.615 36432 Z= 0.311 Chirality : 0.042 0.263 4176 Planarity : 0.004 0.086 4541 Dihedral : 14.018 174.514 4311 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.04 % Allowed : 21.81 % Favored : 76.16 % 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 aren not related in a simple way. whole: -0.88 (0.15), residues: 3174 helix: 1.01 (0.16), residues: 1104 sheet: -1.20 (0.28), residues: 369 loop : -1.57 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 69 TYR 0.017 0.001 TYR H 68 PHE 0.016 0.001 PHE J 668 TRP 0.014 0.001 TRP J 236 HIS 0.007 0.001 HIS J 450 Details of bonding type rmsd covalent geometry : bond 0.00256 (26756) covalent geometry : angle 0.61763 (36420) hydrogen bonds : bond 0.03315 ( 1030) hydrogen bonds : angle 4.30529 ( 2818) metal coordination : bond 0.00150 ( 8) metal coordination : angle 1.40189 ( 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 426 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 371 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 HIS cc_start: 0.7953 (OUTLIER) cc_final: 0.6831 (p-80) REVERT: G 156 SER cc_start: 0.8424 (p) cc_final: 0.8202 (p) REVERT: G 200 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8326 (ptmt) REVERT: I 85 CYS cc_start: 0.8750 (m) cc_final: 0.8350 (m) REVERT: I 274 ILE cc_start: 0.6790 (OUTLIER) cc_final: 0.6382 (tt) REVERT: I 427 ASP cc_start: 0.8185 (m-30) cc_final: 0.7657 (m-30) REVERT: I 472 GLU cc_start: 0.8138 (tp30) cc_final: 0.7785 (tp30) REVERT: I 504 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7739 (tm-30) REVERT: I 1214 ASP cc_start: 0.9127 (t0) cc_final: 0.8918 (t0) REVERT: I 1231 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.8652 (t80) REVERT: I 1274 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7647 (mm-30) REVERT: I 1279 GLU cc_start: 0.8218 (mt-10) cc_final: 0.8010 (mt-10) REVERT: J 133 ARG cc_start: 0.8664 (mmm-85) cc_final: 0.8236 (mmt90) REVERT: J 169 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7774 (tt) REVERT: J 180 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.6725 (tmt) REVERT: J 225 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7817 (mp0) REVERT: J 236 TRP cc_start: 0.8035 (m-10) cc_final: 0.7731 (m-90) REVERT: J 382 TYR cc_start: 0.8977 (m-10) cc_final: 0.8532 (m-10) REVERT: J 684 ASP cc_start: 0.6966 (OUTLIER) cc_final: 0.5815 (m-30) REVERT: J 697 MET cc_start: 0.6219 (tmm) cc_final: 0.5922 (tmm) REVERT: J 806 ASP cc_start: 0.7292 (p0) cc_final: 0.6656 (p0) REVERT: J 1030 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: J 1151 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7743 (tptp) REVERT: J 1188 GLU cc_start: 0.6060 (OUTLIER) cc_final: 0.5569 (tm-30) REVERT: J 1349 GLU cc_start: 0.8464 (mp0) cc_final: 0.8187 (mp0) REVERT: K 60 ASN cc_start: 0.8041 (p0) cc_final: 0.7623 (p0) outliers start: 55 outliers final: 38 residues processed: 405 average time/residue: 0.1617 time to fit residues: 107.0693 Evaluate side-chains 382 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 334 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 131 CYS 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 11 ILE Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 491 ASP 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 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1231 TYR 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 J residue 48 THR 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 573 THR Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 668 PHE Chi-restraints excluded: chain J residue 684 ASP 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 862 THR Chi-restraints excluded: chain J residue 869 CYS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1030 GLU Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1151 LYS Chi-restraints excluded: chain J residue 1163 VAL Chi-restraints excluded: chain J residue 1184 ASP Chi-restraints excluded: chain J residue 1188 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 266 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 187 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 201 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 120 GLN I 165 HIS ** I 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1049 GLN ** K 75 GLN ** 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 = 0.3539 r_free = 0.3539 target = 0.123903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.097691 restraints weight = 49802.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.099194 restraints weight = 29156.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.099667 restraints weight = 21325.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.099866 restraints weight = 19184.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.100055 restraints weight = 18713.126| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26764 Z= 0.148 Angle : 0.638 15.641 36432 Z= 0.323 Chirality : 0.043 0.264 4176 Planarity : 0.004 0.088 4541 Dihedral : 14.034 173.778 4311 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.41 % Allowed : 21.92 % Favored : 75.68 % 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 aren not related in a simple way. whole: -0.87 (0.15), residues: 3174 helix: 1.00 (0.16), residues: 1101 sheet: -1.13 (0.27), residues: 379 loop : -1.55 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 407 TYR 0.022 0.001 TYR G 152 PHE 0.016 0.001 PHE J 668 TRP 0.014 0.001 TRP J1193 HIS 0.009 0.001 HIS J 450 Details of bonding type rmsd covalent geometry : bond 0.00345 (26756) covalent geometry : angle 0.63802 (36420) hydrogen bonds : bond 0.03469 ( 1030) hydrogen bonds : angle 4.34412 ( 2818) metal coordination : bond 0.00570 ( 8) metal coordination : angle 1.32786 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3719.15 seconds wall clock time: 65 minutes 32.62 seconds (3932.62 seconds total)