Starting phenix.real_space_refine on Mon Jul 6 03:52:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mkd_23892/07_2026/7mkd_23892.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mkd_23892/07_2026/7mkd_23892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mkd_23892/07_2026/7mkd_23892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mkd_23892/07_2026/7mkd_23892.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mkd_23892/07_2026/7mkd_23892.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mkd_23892/07_2026/7mkd_23892.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mkd_23892/07_2026/7mkd_23892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mkd_23892/07_2026/7mkd_23892.map" } resolution = 3.2 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= 0.014 sd= 0.111 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 136 5.49 5 Mg 1 5.21 5 S 130 5.16 5 C 19906 2.51 5 N 5727 2.21 5 O 6491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32393 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1808 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain: "H" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1714 Classifications: {'peptide': 223} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1280} Chain: "J" Number of atoms: 10386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10386 Classifications: {'peptide': 1336} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 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: "L" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3847 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 457} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1402 Classifications: {'DNA': 68} Link IDs: {'rna3p': 67} Chain: "Q" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1386 Classifications: {'DNA': 68} Link IDs: {'rna3p': 67} Chain: "R" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14538 SG CYS J 70 101.623 65.647 72.592 1.00101.34 S ATOM 14552 SG CYS J 72 99.864 64.175 69.772 1.00105.00 S ATOM 14660 SG CYS J 85 103.554 65.828 69.277 1.00104.39 S ATOM 14684 SG CYS J 88 100.156 66.070 70.354 1.00102.11 S ATOM 20372 SG CYS J 814 126.393 119.526 106.314 1.00 97.75 S ATOM 20937 SG CYS J 888 123.108 118.015 105.077 1.00 94.17 S ATOM 20988 SG CYS J 895 124.740 116.913 108.396 1.00 87.63 S ATOM 21009 SG CYS J 898 123.059 120.149 108.148 1.00 86.42 S Time building chain proxies: 6.13, per 1000 atoms: 0.19 Number of scatterers: 32393 At special positions: 0 Unit cell: (154.76, 193.98, 191.86, 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 130 16.00 P 136 15.00 Mg 1 11.99 O 6491 8.00 N 5727 7.00 C 19906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 12 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6976 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 51 sheets defined 42.8% alpha, 12.6% beta 53 base pairs and 105 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.732A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 212 through 228 Processing helix chain 'G' and resid 229 through 231 No H-bonds generated for 'chain 'G' and resid 229 through 231' Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.944A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.622A 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 Processing helix chain 'I' and resid 28 through 39 removed outlier: 3.551A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.587A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 197 through 201 removed outlier: 3.780A pdb=" N ARG I 200 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.114A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 288 through 293 Processing helix chain 'I' and resid 318 through 327 removed outlier: 4.025A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) 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 389 removed outlier: 3.761A pdb=" N GLU I 382 " --> pdb=" O ARG I 378 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.609A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 527 removed outlier: 3.929A pdb=" N GLU I 523 " --> pdb=" O ASN I 519 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.885A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 614 removed outlier: 4.139A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.891A 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 670 through 674 Processing helix chain 'I' and resid 676 through 686 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 860 through 865 removed outlier: 3.953A pdb=" N LYS I 864 " --> pdb=" O ALA I 861 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU I 865 " --> pdb=" O LEU I 862 " (cutoff:3.500A) Processing helix chain 'I' and resid 896 through 907 Processing helix chain 'I' and resid 942 through 981 removed outlier: 4.303A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 997 Processing helix chain 'I' and resid 1010 through 1038 removed outlier: 3.679A pdb=" N GLU I1026 " --> pdb=" O LYS I1022 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.542A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1103 removed outlier: 3.504A pdb=" N GLY I1102 " --> pdb=" O ASN I1099 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.508A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 4.056A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.953A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 removed outlier: 3.597A pdb=" N LYS I1242 " --> pdb=" O LEU I1238 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.628A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 4.235A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.712A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.685A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 140 removed outlier: 3.790A pdb=" N ARG J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 192 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 removed outlier: 3.654A pdb=" N TRP J 236 " --> pdb=" O LYS J 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 233 through 236' Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 264 through 286 Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 333 through 335 No H-bonds generated for 'chain 'J' and resid 333 through 335' Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 408 through 417 removed outlier: 3.665A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (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 505 through 514 Processing helix chain 'J' and resid 529 through 539 removed outlier: 3.587A pdb=" N SER J 539 " --> pdb=" O ARG J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 573 through 581 removed outlier: 3.787A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 598 through 613 removed outlier: 3.900A pdb=" N LEU J 605 " --> pdb=" O ILE J 601 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.528A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 removed outlier: 3.879A pdb=" N ILE J 653 " --> pdb=" O LYS J 649 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.265A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 768 through 775 Processing helix chain 'J' and resid 776 through 788 Processing helix chain 'J' and resid 789 through 804 removed outlier: 3.519A pdb=" N ALA J 804 " --> pdb=" O LEU J 800 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.575A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 895 through 900 removed outlier: 3.611A pdb=" N GLY J 900 " --> pdb=" O ALA J 896 " (cutoff:3.500A) Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.586A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 930 Processing helix chain 'J' and resid 1068 through 1073 removed outlier: 3.506A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 removed outlier: 3.671A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1243 removed outlier: 3.867A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1259 removed outlier: 4.388A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.649A pdb=" N ALA J1294 " --> pdb=" O ARG J1290 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1314 Processing helix chain 'J' and resid 1319 through 1324 Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 4.118A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1361 through 1373 removed outlier: 4.536A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.517A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.583A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 78 Processing helix chain 'L' and resid 98 through 106 Processing helix chain 'L' and resid 112 through 136 removed outlier: 3.966A pdb=" N ILE L 117 " --> pdb=" O ARG L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 153 removed outlier: 3.916A pdb=" N ILE L 141 " --> pdb=" O TYR L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 215 through 220 Processing helix chain 'L' and resid 223 through 234 Processing helix chain 'L' and resid 245 through 259 Processing helix chain 'L' and resid 262 through 290 Processing helix chain 'L' and resid 298 through 307 removed outlier: 3.527A pdb=" N THR L 307 " --> pdb=" O ILE L 303 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 323 removed outlier: 4.224A pdb=" N ASN L 323 " --> pdb=" O ILE L 320 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 329 Processing helix chain 'L' and resid 330 through 332 No H-bonds generated for 'chain 'L' and resid 330 through 332' Processing helix chain 'L' and resid 333 through 352 Processing helix chain 'L' and resid 354 through 383 Processing helix chain 'L' and resid 383 through 394 removed outlier: 3.977A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR L 394 " --> pdb=" O ILE L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 419 Processing helix chain 'L' and resid 420 through 424 removed outlier: 3.921A pdb=" N ARG L 423 " --> pdb=" O GLU L 420 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY L 424 " --> pdb=" O TYR L 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 420 through 424' Processing helix chain 'L' and resid 426 through 447 removed outlier: 4.278A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 removed outlier: 3.919A pdb=" N GLN L 472 " --> pdb=" O ARG L 468 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU L 473 " --> pdb=" O GLN L 469 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET L 474 " --> pdb=" O MET L 470 " (cutoff:3.500A) Processing helix chain 'L' and resid 479 through 487 removed outlier: 3.668A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) Processing helix chain 'L' and resid 492 through 499 Processing helix chain 'L' and resid 518 through 522 Processing helix chain 'L' and resid 530 through 549 Processing helix chain 'L' and resid 552 through 563 removed outlier: 3.691A pdb=" N PHE L 563 " --> pdb=" O LEU L 559 " (cutoff:3.500A) Processing helix chain 'L' and resid 572 through 581 Processing helix chain 'L' and resid 583 through 600 removed outlier: 3.501A pdb=" N HIS L 600 " --> pdb=" O ARG L 596 " (cutoff:3.500A) Processing helix chain 'L' and resid 603 through 609 removed outlier: 4.101A pdb=" N LEU L 607 " --> pdb=" O ARG L 603 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 261 removed outlier: 3.569A pdb=" N GLU R 261 " --> pdb=" O ASP R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 273 Processing helix chain 'R' and resid 277 through 284 removed outlier: 4.330A pdb=" N ARG R 284 " --> pdb=" O ASP R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 291 Processing helix chain 'R' and resid 296 through 310 removed outlier: 3.561A pdb=" N LEU R 300 " --> pdb=" O GLY R 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 20 removed outlier: 3.903A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLN G 18 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE G 183 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 99 removed outlier: 6.765A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'G' and resid 102 through 105 Processing sheet with id=AA6, first strand: chain 'G' and resid 108 through 110 removed outlier: 3.731A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 13 through 17 removed outlier: 3.624A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR H 27 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLU H 29 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU H 201 " --> pdb=" O GLU H 29 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.632A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AB1, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB2, first strand: chain 'H' and resid 109 through 111 removed outlier: 7.002A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB4, first strand: chain 'H' and resid 180 through 183 removed outlier: 6.546A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.630A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.825A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB8, first strand: chain 'I' and resid 147 through 148 removed outlier: 6.419A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 154 through 155 Processing sheet with id=AC1, first strand: chain 'I' and resid 195 through 196 Processing sheet with id=AC2, first strand: chain 'I' and resid 227 through 231 removed outlier: 3.532A pdb=" N ILE I 333 " --> pdb=" O PHE I 230 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 238 through 240 Processing sheet with id=AC4, first strand: chain 'I' and resid 255 through 257 removed outlier: 7.176A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.892A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU I 308 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.306A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC8, first strand: chain 'I' and resid 633 through 637 Processing sheet with id=AC9, first strand: chain 'I' and resid 748 through 752 removed outlier: 3.765A pdb=" N ARG I 731 " --> pdb=" O ASP I 728 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AD2, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AD3, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AD4, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 3.760A pdb=" N ALA I1067 " --> pdb=" O LEU I1233 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.704A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP I 842 " --> pdb=" O VAL I1046 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL I1046 " --> pdb=" O ASP I 842 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.951A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AD8, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 6.289A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AE1, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AE2, first strand: chain 'I' and resid 1335 through 1340 Processing sheet with id=AE3, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.586A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 9.826A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AE5, first strand: chain 'J' and resid 252 through 255 removed outlier: 3.966A pdb=" N ARG J 259 " --> pdb=" O LEU J 255 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 548 through 556 Processing sheet with id=AE7, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AE8, first strand: chain 'J' and resid 821 through 822 Processing sheet with id=AE9, first strand: chain 'J' and resid 825 through 826 removed outlier: 7.051A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 991 through 996 removed outlier: 3.933A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 965 through 967 removed outlier: 3.648A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL J1002 " --> pdb=" O ASN J1019 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN J1019 " --> pdb=" O VAL J1002 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 1033 through 1034 Processing sheet with id=AF4, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 4.014A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 1187 through 1191 Processing sheet with id=AF6, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.882A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1244 hydrogen bonds defined for protein. 3498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 133 hydrogen bonds 266 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 105 stacking parallelities Total time for adding SS restraints: 7.89 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 5315 1.26 - 1.41: 7725 1.41 - 1.55: 19569 1.55 - 1.69: 318 1.69 - 1.83: 237 Bond restraints: 33164 Sorted by residual: bond pdb=" C19 1N7 I1402 " pdb=" C3 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.826 -0.294 2.00e-02 2.50e+03 2.16e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.817 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C19 1N7 Q 101 " pdb=" C3 1N7 Q 101 " ideal model delta sigma weight residual 1.532 1.816 -0.284 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C3 1N7 I1402 " pdb=" C4 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.735 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C3 1N7 Q 101 " pdb=" C4 1N7 Q 101 " ideal model delta sigma weight residual 1.532 1.723 -0.191 2.00e-02 2.50e+03 9.11e+01 ... (remaining 33159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 44503 2.56 - 5.12: 778 5.12 - 7.67: 80 7.67 - 10.23: 18 10.23 - 12.79: 5 Bond angle restraints: 45384 Sorted by residual: angle pdb=" N GLU J 86 " pdb=" CA GLU J 86 " pdb=" C GLU J 86 " ideal model delta sigma weight residual 111.14 121.92 -10.78 1.08e+00 8.57e-01 9.96e+01 angle pdb=" N GLU J 713 " pdb=" CA GLU J 713 " pdb=" C GLU J 713 " ideal model delta sigma weight residual 110.53 122.51 -11.98 1.32e+00 5.74e-01 8.24e+01 angle pdb=" C GLU L 503 " pdb=" N PRO L 504 " pdb=" CA PRO L 504 " ideal model delta sigma weight residual 119.84 130.10 -10.26 1.25e+00 6.40e-01 6.74e+01 angle pdb=" C VAL J 90 " pdb=" CA VAL J 90 " pdb=" CB VAL J 90 " ideal model delta sigma weight residual 110.96 101.31 9.65 1.21e+00 6.83e-01 6.36e+01 angle pdb=" C ILE I1210 " pdb=" CA ILE I1210 " pdb=" CB ILE I1210 " ideal model delta sigma weight residual 111.29 98.50 12.79 1.64e+00 3.72e-01 6.08e+01 ... (remaining 45379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 18987 34.45 - 68.90: 1015 68.90 - 103.36: 38 103.36 - 137.81: 0 137.81 - 172.26: 1 Dihedral angle restraints: 20041 sinusoidal: 9223 harmonic: 10818 Sorted by residual: dihedral pdb=" CA PHE J1325 " pdb=" C PHE J1325 " pdb=" N GLN J1326 " pdb=" CA GLN J1326 " ideal model delta harmonic sigma weight residual 180.00 136.30 43.70 0 5.00e+00 4.00e-02 7.64e+01 dihedral pdb=" CA ASP J1184 " pdb=" C ASP J1184 " pdb=" N PRO J1185 " pdb=" CA PRO J1185 " ideal model delta harmonic sigma weight residual -180.00 -143.95 -36.05 0 5.00e+00 4.00e-02 5.20e+01 dihedral pdb=" CA SER J 119 " pdb=" C SER J 119 " pdb=" N LEU J 120 " pdb=" CA LEU J 120 " ideal model delta harmonic sigma weight residual -180.00 -146.53 -33.47 0 5.00e+00 4.00e-02 4.48e+01 ... (remaining 20038 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4858 0.100 - 0.201: 316 0.201 - 0.301: 15 0.301 - 0.401: 5 0.401 - 0.501: 4 Chirality restraints: 5198 Sorted by residual: chirality pdb=" CA SER L 89 " pdb=" N SER L 89 " pdb=" C SER L 89 " pdb=" CB SER L 89 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.28e+00 chirality pdb=" C19 1N7 I1402 " pdb=" C18 1N7 I1402 " pdb=" C2 1N7 I1402 " pdb=" C3 1N7 I1402 " both_signs ideal model delta sigma weight residual False -2.53 -3.02 0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" C19 1N7 Q 101 " pdb=" C18 1N7 Q 101 " pdb=" C2 1N7 Q 101 " pdb=" C3 1N7 Q 101 " both_signs ideal model delta sigma weight residual False -2.53 -2.99 0.45 2.00e-01 2.50e+01 5.15e+00 ... (remaining 5195 not shown) Planarity restraints: 5427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE J1325 " 0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C PHE J1325 " -0.072 2.00e-02 2.50e+03 pdb=" O PHE J1325 " 0.028 2.00e-02 2.50e+03 pdb=" N GLN J1326 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG G 235 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C ARG G 235 " 0.054 2.00e-02 2.50e+03 pdb=" O ARG G 235 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP G 236 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR J 705 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.60e+00 pdb=" C THR J 705 " -0.048 2.00e-02 2.50e+03 pdb=" O THR J 705 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL J 706 " 0.016 2.00e-02 2.50e+03 ... (remaining 5424 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 33 2.30 - 2.95: 14707 2.95 - 3.60: 45548 3.60 - 4.25: 72011 4.25 - 4.90: 122607 Nonbonded interactions: 254906 Sorted by model distance: nonbonded pdb=" NZ LYS J 74 " pdb=" NZ LYS J 87 " model vdw 1.653 3.200 nonbonded pdb=" O ASP I 516 " pdb=" OD1 ASP I 516 " model vdw 2.074 3.040 nonbonded pdb=" OG1 THR J 844 " pdb=" O ARG J 860 " model vdw 2.163 3.040 nonbonded pdb=" N ASP J 751 " pdb=" OD1 ASP J 751 " model vdw 2.165 3.120 nonbonded pdb=" O SER J 775 " pdb=" OG SER J 775 " model vdw 2.174 3.040 ... (remaining 254901 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 5 through 158 or resid 167 through 233)) selection = (chain 'H' and resid 5 through 233) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 35.040 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.012 1.038 33172 Z= 0.570 Angle : 0.920 49.709 45396 Z= 0.558 Chirality : 0.056 0.501 5198 Planarity : 0.005 0.092 5427 Dihedral : 17.860 172.262 13065 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.18 % Favored : 92.77 % Rotamer: Outliers : 6.15 % Allowed : 10.85 % Favored : 83.00 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.13), residues: 3732 helix: 0.30 (0.14), residues: 1450 sheet: -2.02 (0.24), residues: 444 loop : -1.93 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J1290 TYR 0.021 0.002 TYR G 177 PHE 0.017 0.002 PHE I 186 TRP 0.009 0.001 TRP I1276 HIS 0.006 0.001 HIS J 80 Details of bonding type rmsd/Z covalent geometry : bond 0.01025 / 0.53 (33164) covalent geometry : angle 0.85760 / 0.55 (45384) hydrogen bonds : bond 0.16476 / 11.38 ( 1371) hydrogen bonds : angle 6.26924 / 4.35 ( 3764) metal coordination : bond 0.36736 / 18.37 ( 8) metal coordination : angle 20.42486 / 11.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 238 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 83 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8597 (mp) REVERT: I 315 MET cc_start: 0.8352 (ttp) cc_final: 0.7715 (ptm) REVERT: I 332 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7804 (mtp85) REVERT: I 538 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8880 (pp) REVERT: I 768 MET cc_start: 0.7699 (mtm) cc_final: 0.7414 (mtm) REVERT: I 979 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7663 (mp) REVERT: I 1157 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8393 (pp30) REVERT: I 1161 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8038 (mp) REVERT: I 1327 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8052 (mp) REVERT: J 81 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8501 (tmm-80) REVERT: J 196 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8250 (tm-30) REVERT: J 267 ASP cc_start: 0.8140 (t70) cc_final: 0.7834 (t0) REVERT: J 342 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9083 (mt) REVERT: J 497 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8182 (mt-10) REVERT: J 789 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7142 (ptmt) REVERT: J 802 ASP cc_start: 0.7797 (m-30) cc_final: 0.7544 (m-30) REVERT: J 849 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7772 (pp) REVERT: J 903 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7780 (mp) REVERT: K 43 ASN cc_start: 0.8600 (t0) cc_final: 0.8270 (t0) REVERT: K 70 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7644 (tm-30) REVERT: L 89 SER cc_start: 0.7553 (OUTLIER) cc_final: 0.7186 (p) REVERT: L 93 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7816 (mtp-110) REVERT: L 100 MET cc_start: 0.8858 (mtt) cc_final: 0.8568 (mtm) REVERT: L 216 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7845 (pp) REVERT: L 277 MET cc_start: 0.8091 (tpt) cc_final: 0.7412 (tpp) REVERT: L 567 MET cc_start: 0.8483 (mtm) cc_final: 0.8101 (mtm) outliers start: 198 outliers final: 105 residues processed: 426 average time/residue: 0.1760 time to fit residues: 123.9207 Evaluate side-chains 328 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 209 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 17 LYS Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 610 GLU Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 748 ILE Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 963 GLU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1088 ASP Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain I residue 1341 ASP Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 85 CYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 594 GLN Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 753 SER Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 789 LYS Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain L residue 93 ARG Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 452 ILE Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 581 ASP Chi-restraints excluded: chain L residue 591 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 93 GLN I 276 GLN I 761 GLN I 799 ASN I 856 ASN ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN J 300 GLN J 777 HIS J1244 GLN L 437 GLN L 464 ASN L 472 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.131279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.074897 restraints weight = 50787.974| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.78 r_work: 0.2803 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33172 Z= 0.136 Angle : 0.634 28.958 45396 Z= 0.330 Chirality : 0.043 0.250 5198 Planarity : 0.005 0.058 5427 Dihedral : 18.497 175.579 5832 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.11 % Rotamer: Outliers : 4.13 % Allowed : 13.39 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.14), residues: 3732 helix: 0.89 (0.14), residues: 1487 sheet: -1.78 (0.24), residues: 435 loop : -1.76 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG J 709 TYR 0.016 0.001 TYR G 177 PHE 0.016 0.001 PHE I 337 TRP 0.008 0.001 TRP L 315 HIS 0.003 0.001 HIS J1252 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (33164) covalent geometry : angle 0.60790 / 0.33 (45384) hydrogen bonds : bond 0.04644 / 3.17 ( 1371) hydrogen bonds : angle 4.73528 / 3.28 ( 3764) metal coordination : bond 0.01558 / 0.69 ( 8) metal coordination : angle 11.05812 / 6.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 243 time to evaluate : 1.163 Fit side-chains REVERT: G 212 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7279 (t0) REVERT: H 66 HIS cc_start: 0.7891 (t-170) cc_final: 0.7490 (t-90) REVERT: I 332 ARG cc_start: 0.7896 (mtp85) cc_final: 0.7671 (mtp85) REVERT: I 337 PHE cc_start: 0.8892 (t80) cc_final: 0.8661 (t80) REVERT: I 538 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8529 (pp) REVERT: I 704 MET cc_start: 0.8436 (mmm) cc_final: 0.8221 (tpp) REVERT: I 768 MET cc_start: 0.7725 (mtm) cc_final: 0.7382 (mtm) REVERT: I 979 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7165 (mp) REVERT: I 1157 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8219 (pp30) REVERT: I 1327 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7733 (mp) REVERT: J 267 ASP cc_start: 0.8249 (t70) cc_final: 0.7916 (t0) REVERT: J 300 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7431 (tp-100) REVERT: J 457 TYR cc_start: 0.8748 (m-80) cc_final: 0.8490 (m-80) REVERT: J 497 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8469 (mt-10) REVERT: J 731 ARG cc_start: 0.8705 (tpt-90) cc_final: 0.8318 (tpp-160) REVERT: J 736 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7466 (mp10) REVERT: J 802 ASP cc_start: 0.7684 (m-30) cc_final: 0.7442 (m-30) REVERT: J 849 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7669 (pp) REVERT: J 903 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7445 (mp) REVERT: J 907 HIS cc_start: 0.8137 (p90) cc_final: 0.7883 (p-80) REVERT: J 1189 MET cc_start: 0.8360 (mmp) cc_final: 0.8080 (mmp) REVERT: J 1193 TRP cc_start: 0.8755 (p90) cc_final: 0.8347 (p90) REVERT: K 43 ASN cc_start: 0.8687 (t0) cc_final: 0.8235 (t0) REVERT: K 70 GLN cc_start: 0.7514 (tm-30) cc_final: 0.7268 (tm-30) REVERT: K 71 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7574 (mm-30) REVERT: L 89 SER cc_start: 0.6725 (OUTLIER) cc_final: 0.6232 (p) REVERT: L 93 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8047 (mtp-110) REVERT: L 259 PHE cc_start: 0.7776 (m-80) cc_final: 0.7353 (m-80) REVERT: L 277 MET cc_start: 0.7941 (tpt) cc_final: 0.7314 (tpp) REVERT: L 474 MET cc_start: 0.8820 (ptm) cc_final: 0.8445 (ptm) REVERT: L 476 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7848 (pmt-80) REVERT: L 567 MET cc_start: 0.8319 (mtm) cc_final: 0.7942 (mtm) outliers start: 133 outliers final: 77 residues processed: 362 average time/residue: 0.1831 time to fit residues: 108.0750 Evaluate side-chains 309 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 220 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 856 ASN Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 300 GLN Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 736 GLN Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 93 ARG Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 591 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 92 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 chunk 144 optimal weight: 20.0000 chunk 368 optimal weight: 30.0000 chunk 139 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 190 optimal weight: 0.3980 chunk 33 optimal weight: 8.9990 chunk 341 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 overall best weight: 5.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 856 ASN J 157 GLN J 186 GLN ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 472 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.127207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.070770 restraints weight = 51379.721| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.75 r_work: 0.2731 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 33172 Z= 0.369 Angle : 0.730 21.179 45396 Z= 0.381 Chirality : 0.048 0.265 5198 Planarity : 0.005 0.054 5427 Dihedral : 18.518 175.478 5739 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.69 % Favored : 92.26 % Rotamer: Outliers : 4.94 % Allowed : 14.76 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3732 helix: 0.89 (0.14), residues: 1473 sheet: -1.86 (0.24), residues: 421 loop : -1.84 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J1203 TYR 0.020 0.002 TYR G 177 PHE 0.019 0.002 PHE J 437 TRP 0.008 0.001 TRP L 315 HIS 0.006 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00888 / 0.37 (33164) covalent geometry : angle 0.71874 / 0.38 (45384) hydrogen bonds : bond 0.05423 / 3.69 ( 1371) hydrogen bonds : angle 4.70999 / 3.26 ( 3764) metal coordination : bond 0.01725 / 0.96 ( 8) metal coordination : angle 7.81086 / 4.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 218 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: G 228 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7274 (mp) REVERT: H 66 HIS cc_start: 0.7914 (t-170) cc_final: 0.7468 (t-90) REVERT: I 47 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.7922 (p90) REVERT: I 315 MET cc_start: 0.8305 (ttp) cc_final: 0.7469 (ptm) REVERT: I 332 ARG cc_start: 0.7942 (mtp85) cc_final: 0.7719 (mtp85) REVERT: I 529 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7951 (mtt-85) REVERT: I 538 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8565 (pp) REVERT: I 768 MET cc_start: 0.7883 (mtm) cc_final: 0.7522 (mtm) REVERT: I 979 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7187 (mp) REVERT: I 1157 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8551 (pp30) REVERT: I 1269 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8773 (ttt90) REVERT: I 1327 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7780 (mp) REVERT: J 196 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8153 (tm-30) REVERT: J 267 ASP cc_start: 0.8470 (t70) cc_final: 0.8019 (t0) REVERT: J 736 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7969 (mp10) REVERT: J 802 ASP cc_start: 0.7941 (m-30) cc_final: 0.7691 (m-30) REVERT: J 849 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7639 (pp) REVERT: J 903 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7670 (mp) REVERT: J 907 HIS cc_start: 0.8169 (p90) cc_final: 0.7921 (p-80) REVERT: J 1193 TRP cc_start: 0.8713 (p90) cc_final: 0.8238 (p90) REVERT: K 43 ASN cc_start: 0.8841 (t0) cc_final: 0.8412 (t0) REVERT: K 46 THR cc_start: 0.7631 (OUTLIER) cc_final: 0.7426 (m) REVERT: K 70 GLN cc_start: 0.7566 (tm-30) cc_final: 0.7319 (tm-30) REVERT: L 89 SER cc_start: 0.6851 (OUTLIER) cc_final: 0.6409 (p) REVERT: L 93 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7951 (mtp-110) REVERT: L 273 MET cc_start: 0.8865 (mmp) cc_final: 0.8596 (mmp) REVERT: L 277 MET cc_start: 0.7941 (tpt) cc_final: 0.7343 (tpp) REVERT: L 474 MET cc_start: 0.8765 (ptm) cc_final: 0.8412 (ptm) REVERT: L 476 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7844 (pmt-80) REVERT: L 567 MET cc_start: 0.8368 (mtm) cc_final: 0.8001 (mtm) outliers start: 159 outliers final: 114 residues processed: 364 average time/residue: 0.2060 time to fit residues: 122.9541 Evaluate side-chains 341 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 212 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 529 ARG Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 888 THR Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1019 ASP Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1269 ARG Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 736 GLN Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 874 GLU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 93 ARG Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 236 LYS Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 487 MET Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 591 GLU Chi-restraints excluded: chain L residue 609 SER Chi-restraints excluded: chain R residue 260 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 104 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 361 optimal weight: 3.9990 chunk 331 optimal weight: 30.0000 chunk 310 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 318 optimal weight: 6.9990 chunk 246 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 157 GLN J 720 ASN L 472 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.130535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.074188 restraints weight = 50650.208| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.76 r_work: 0.2793 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33172 Z= 0.152 Angle : 0.585 14.324 45396 Z= 0.312 Chirality : 0.043 0.259 5198 Planarity : 0.004 0.052 5427 Dihedral : 18.324 174.690 5737 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.73 % Favored : 94.21 % Rotamer: Outliers : 4.32 % Allowed : 15.66 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.14), residues: 3732 helix: 1.16 (0.14), residues: 1487 sheet: -1.69 (0.24), residues: 436 loop : -1.68 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 260 TYR 0.023 0.001 TYR L 148 PHE 0.023 0.001 PHE L 165 TRP 0.008 0.001 TRP L 315 HIS 0.003 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (33164) covalent geometry : angle 0.57847 / 0.31 (45384) hydrogen bonds : bond 0.04190 / 2.85 ( 1371) hydrogen bonds : angle 4.37973 / 3.03 ( 3764) metal coordination : bond 0.00694 / 0.38 ( 8) metal coordination : angle 5.54806 / 3.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 229 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: G 212 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7318 (t0) REVERT: H 66 HIS cc_start: 0.7960 (t-170) cc_final: 0.7646 (t-90) REVERT: I 315 MET cc_start: 0.8230 (ttp) cc_final: 0.7468 (ptm) REVERT: I 332 ARG cc_start: 0.7935 (mtp85) cc_final: 0.7720 (mtp85) REVERT: I 538 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8551 (pp) REVERT: I 768 MET cc_start: 0.7845 (mtm) cc_final: 0.7539 (mtm) REVERT: I 979 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7154 (mp) REVERT: I 1157 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8370 (pp30) REVERT: I 1327 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7734 (mp) REVERT: J 196 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7821 (tm-30) REVERT: J 267 ASP cc_start: 0.8303 (t70) cc_final: 0.7919 (t0) REVERT: J 497 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8539 (mt-10) REVERT: J 709 ARG cc_start: 0.7134 (ppt170) cc_final: 0.6840 (ppt170) REVERT: J 731 ARG cc_start: 0.8716 (tpt-90) cc_final: 0.8319 (tpp-160) REVERT: J 736 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7474 (mp10) REVERT: J 802 ASP cc_start: 0.7702 (m-30) cc_final: 0.7500 (m-30) REVERT: J 849 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7661 (pp) REVERT: J 903 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7584 (mp) REVERT: J 907 HIS cc_start: 0.8157 (p90) cc_final: 0.7859 (p-80) REVERT: J 1193 TRP cc_start: 0.8756 (p90) cc_final: 0.8336 (p90) REVERT: K 43 ASN cc_start: 0.8805 (t0) cc_final: 0.8320 (t0) REVERT: K 70 GLN cc_start: 0.7514 (tm-30) cc_final: 0.7305 (tm-30) REVERT: L 89 SER cc_start: 0.6863 (OUTLIER) cc_final: 0.6529 (p) REVERT: L 277 MET cc_start: 0.7958 (tpt) cc_final: 0.7361 (tpp) REVERT: L 474 MET cc_start: 0.8724 (ptm) cc_final: 0.8386 (ptm) REVERT: L 476 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7867 (pmt-80) REVERT: L 567 MET cc_start: 0.8272 (mtm) cc_final: 0.7930 (mtm) outliers start: 139 outliers final: 95 residues processed: 357 average time/residue: 0.1948 time to fit residues: 115.0834 Evaluate side-chains 326 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 221 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 736 GLN Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 236 LYS Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 487 MET Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 591 GLU Chi-restraints excluded: chain R residue 260 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 200 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 362 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 297 optimal weight: 9.9990 chunk 252 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 222 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 93 GLN J1098 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.130662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.074201 restraints weight = 50880.308| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.78 r_work: 0.2793 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33172 Z= 0.162 Angle : 0.577 11.105 45396 Z= 0.307 Chirality : 0.042 0.260 5198 Planarity : 0.004 0.047 5427 Dihedral : 18.241 174.934 5729 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.35 % Favored : 93.60 % Rotamer: Outliers : 4.47 % Allowed : 16.10 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.68 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.14), residues: 3732 helix: 1.26 (0.14), residues: 1501 sheet: -1.59 (0.25), residues: 429 loop : -1.59 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 473 TYR 0.030 0.001 TYR L 148 PHE 0.016 0.001 PHE J1165 TRP 0.016 0.001 TRP L 326 HIS 0.003 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (33164) covalent geometry : angle 0.57323 / 0.31 (45384) hydrogen bonds : bond 0.04082 / 2.78 ( 1371) hydrogen bonds : angle 4.24176 / 2.92 ( 3764) metal coordination : bond 0.00659 / 0.39 ( 8) metal coordination : angle 4.29876 / 2.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 230 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: G 129 VAL cc_start: 0.8715 (OUTLIER) cc_final: 0.8512 (t) REVERT: G 212 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7284 (t0) REVERT: G 228 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7098 (mp) REVERT: H 66 HIS cc_start: 0.7997 (t-170) cc_final: 0.7687 (t-90) REVERT: I 315 MET cc_start: 0.8239 (ttp) cc_final: 0.7471 (ptm) REVERT: I 332 ARG cc_start: 0.7946 (mtp85) cc_final: 0.7736 (mtp85) REVERT: I 538 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8560 (pp) REVERT: I 768 MET cc_start: 0.7835 (mtm) cc_final: 0.7516 (mtm) REVERT: I 781 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8193 (m-30) REVERT: I 979 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7153 (mp) REVERT: I 1157 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8422 (pp30) REVERT: I 1269 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8763 (ttt90) REVERT: I 1327 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7797 (mp) REVERT: J 196 GLN cc_start: 0.8294 (tm-30) cc_final: 0.7832 (tm-30) REVERT: J 197 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7033 (tt0) REVERT: J 267 ASP cc_start: 0.8285 (t70) cc_final: 0.7902 (t0) REVERT: J 497 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8551 (mt-10) REVERT: J 709 ARG cc_start: 0.7287 (ppt170) cc_final: 0.6926 (ppt170) REVERT: J 731 ARG cc_start: 0.8681 (tpt-90) cc_final: 0.8296 (tpp-160) REVERT: J 736 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7347 (mp10) REVERT: J 802 ASP cc_start: 0.7721 (m-30) cc_final: 0.7507 (m-30) REVERT: J 849 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7689 (pp) REVERT: J 867 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8227 (mp10) REVERT: J 903 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7636 (mp) REVERT: J 907 HIS cc_start: 0.8087 (p90) cc_final: 0.7738 (p-80) REVERT: J 1193 TRP cc_start: 0.8732 (p90) cc_final: 0.8293 (p90) REVERT: K 43 ASN cc_start: 0.8837 (t0) cc_final: 0.8334 (t0) REVERT: L 89 SER cc_start: 0.6843 (OUTLIER) cc_final: 0.6579 (p) REVERT: L 96 ASP cc_start: 0.7964 (t0) cc_final: 0.7733 (t70) REVERT: L 277 MET cc_start: 0.7918 (tpt) cc_final: 0.7345 (tpp) REVERT: L 288 MET cc_start: 0.7099 (tmm) cc_final: 0.6730 (tmm) REVERT: L 474 MET cc_start: 0.8606 (ptm) cc_final: 0.8248 (ptm) REVERT: L 476 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7765 (pmt-80) REVERT: L 567 MET cc_start: 0.8279 (mtm) cc_final: 0.7910 (mtm) outliers start: 144 outliers final: 112 residues processed: 361 average time/residue: 0.1881 time to fit residues: 112.0383 Evaluate side-chains 352 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 224 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 610 GLU Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1019 ASP Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1157 GLN Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1269 ARG Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 347 VAL Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 736 GLN Chi-restraints excluded: chain J residue 754 ILE Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 867 GLN Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 353 LEU Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 487 MET Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 591 GLU Chi-restraints excluded: chain L residue 595 LEU Chi-restraints excluded: chain L residue 609 SER Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain R residue 260 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 258 optimal weight: 0.3980 chunk 262 optimal weight: 0.5980 chunk 188 optimal weight: 0.4980 chunk 284 optimal weight: 50.0000 chunk 268 optimal weight: 6.9990 chunk 293 optimal weight: 8.9990 chunk 227 optimal weight: 0.4980 chunk 290 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 209 optimal weight: 7.9990 chunk 206 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 93 GLN ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN ** J1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.133852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.077789 restraints weight = 50377.929| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.75 r_work: 0.2863 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 33172 Z= 0.105 Angle : 0.538 10.787 45396 Z= 0.288 Chirality : 0.041 0.257 5198 Planarity : 0.004 0.047 5427 Dihedral : 17.999 174.710 5726 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.20 % Rotamer: Outliers : 3.92 % Allowed : 17.06 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3732 helix: 1.48 (0.14), residues: 1513 sheet: -1.42 (0.25), residues: 424 loop : -1.43 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 473 TYR 0.016 0.001 TYR L 148 PHE 0.021 0.001 PHE L 259 TRP 0.011 0.001 TRP J1020 HIS 0.003 0.000 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (33164) covalent geometry : angle 0.53442 / 0.29 (45384) hydrogen bonds : bond 0.03426 / 2.34 ( 1371) hydrogen bonds : angle 4.00337 / 2.75 ( 3764) metal coordination : bond 0.00403 / 0.21 ( 8) metal coordination : angle 3.62626 / 2.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 263 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: G 212 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7216 (t0) REVERT: H 66 HIS cc_start: 0.8002 (t-170) cc_final: 0.7673 (t-90) REVERT: H 75 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: H 103 ASN cc_start: 0.8901 (t0) cc_final: 0.8623 (t0) REVERT: I 315 MET cc_start: 0.8117 (ttp) cc_final: 0.7393 (ptm) REVERT: I 414 ILE cc_start: 0.9395 (pt) cc_final: 0.9172 (pt) REVERT: I 524 ILE cc_start: 0.8631 (tt) cc_final: 0.8429 (tt) REVERT: I 538 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8537 (pp) REVERT: I 704 MET cc_start: 0.7858 (mmm) cc_final: 0.7571 (tpp) REVERT: I 781 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8169 (m-30) REVERT: I 1327 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7956 (mp) REVERT: I 1340 GLU cc_start: 0.7885 (pp20) cc_final: 0.7339 (pt0) REVERT: J 196 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7787 (tm-30) REVERT: J 197 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7032 (tt0) REVERT: J 227 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.6613 (t80) REVERT: J 267 ASP cc_start: 0.8145 (t70) cc_final: 0.7863 (t0) REVERT: J 497 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8605 (mt-10) REVERT: J 731 ARG cc_start: 0.8620 (tpt-90) cc_final: 0.8215 (tpp-160) REVERT: J 849 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7548 (pp) REVERT: J 907 HIS cc_start: 0.8218 (p90) cc_final: 0.7800 (p-80) REVERT: J 1193 TRP cc_start: 0.8739 (p90) cc_final: 0.8380 (p90) REVERT: K 43 ASN cc_start: 0.8782 (t0) cc_final: 0.8255 (t0) REVERT: L 273 MET cc_start: 0.8855 (mmp) cc_final: 0.8636 (mmm) REVERT: L 276 MET cc_start: 0.8876 (mmm) cc_final: 0.8356 (mtp) REVERT: L 277 MET cc_start: 0.7887 (tpt) cc_final: 0.7331 (tpp) REVERT: L 288 MET cc_start: 0.7429 (tmm) cc_final: 0.7184 (tmm) REVERT: L 474 MET cc_start: 0.8571 (ptm) cc_final: 0.8273 (ptm) REVERT: L 476 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7913 (pmt-80) REVERT: L 567 MET cc_start: 0.8234 (mtm) cc_final: 0.7881 (mtm) outliers start: 126 outliers final: 83 residues processed: 374 average time/residue: 0.1856 time to fit residues: 115.4287 Evaluate side-chains 328 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 236 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1019 ASP Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 365 GLN Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 353 LEU Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 609 SER Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain R residue 260 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 33 optimal weight: 8.9990 chunk 220 optimal weight: 3.9990 chunk 251 optimal weight: 0.9980 chunk 376 optimal weight: 40.0000 chunk 349 optimal weight: 4.9990 chunk 368 optimal weight: 30.0000 chunk 181 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 320 optimal weight: 7.9990 chunk 300 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 31 GLN L 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.130356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.073913 restraints weight = 50895.812| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.77 r_work: 0.2788 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 33172 Z= 0.228 Angle : 0.599 9.908 45396 Z= 0.316 Chirality : 0.044 0.266 5198 Planarity : 0.004 0.049 5427 Dihedral : 18.027 175.213 5696 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.27 % Favored : 93.68 % Rotamer: Outliers : 3.95 % Allowed : 17.84 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.14), residues: 3732 helix: 1.48 (0.14), residues: 1503 sheet: -1.43 (0.25), residues: 425 loop : -1.44 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 77 TYR 0.017 0.001 TYR G 177 PHE 0.014 0.001 PHE I 186 TRP 0.009 0.001 TRP J1020 HIS 0.008 0.001 HIS J 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 (33164) covalent geometry : angle 0.59625 / 0.32 (45384) hydrogen bonds : bond 0.04092 / 2.77 ( 1371) hydrogen bonds : angle 4.08675 / 2.81 ( 3764) metal coordination : bond 0.00850 / 0.51 ( 8) metal coordination : angle 3.37768 / 1.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 234 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 212 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7297 (t0) REVERT: G 228 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7054 (mp) REVERT: H 66 HIS cc_start: 0.8030 (t-170) cc_final: 0.7638 (t-90) REVERT: H 75 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: I 47 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.7935 (p90) REVERT: I 276 GLN cc_start: 0.8826 (mt0) cc_final: 0.8453 (tm-30) REVERT: I 315 MET cc_start: 0.8206 (ttp) cc_final: 0.7441 (ptm) REVERT: I 332 ARG cc_start: 0.7925 (mtp85) cc_final: 0.7134 (mtp85) REVERT: I 414 ILE cc_start: 0.9401 (pt) cc_final: 0.9177 (pt) REVERT: I 529 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7875 (mtt-85) REVERT: I 538 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8575 (pp) REVERT: I 637 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.5580 (ptm-80) REVERT: I 1327 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7892 (mp) REVERT: I 1340 GLU cc_start: 0.7868 (pp20) cc_final: 0.7390 (pt0) REVERT: J 196 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7818 (tm-30) REVERT: J 197 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7018 (tt0) REVERT: J 267 ASP cc_start: 0.8326 (t70) cc_final: 0.7988 (t0) REVERT: J 497 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8643 (mt-10) REVERT: J 709 ARG cc_start: 0.6967 (ppt170) cc_final: 0.6747 (ppt170) REVERT: J 731 ARG cc_start: 0.8735 (tpt-90) cc_final: 0.8366 (tpp-160) REVERT: J 849 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7582 (pp) REVERT: J 867 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8263 (mp10) REVERT: J 907 HIS cc_start: 0.8079 (p90) cc_final: 0.7680 (p-80) REVERT: J 1193 TRP cc_start: 0.8748 (p90) cc_final: 0.8357 (p90) REVERT: K 25 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6680 (ttp-110) REVERT: K 43 ASN cc_start: 0.8882 (t0) cc_final: 0.8206 (t0) REVERT: L 277 MET cc_start: 0.7891 (tpt) cc_final: 0.7350 (tpp) REVERT: L 288 MET cc_start: 0.7393 (tmm) cc_final: 0.7160 (tmm) REVERT: L 474 MET cc_start: 0.8598 (ptm) cc_final: 0.8329 (ptm) REVERT: L 476 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7819 (pmt-80) REVERT: L 567 MET cc_start: 0.8271 (mtm) cc_final: 0.7968 (mtm) outliers start: 127 outliers final: 102 residues processed: 351 average time/residue: 0.1974 time to fit residues: 113.3971 Evaluate side-chains 344 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 229 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 529 ARG Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1019 ASP Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 867 GLN Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 236 LYS Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 609 SER Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain R residue 260 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 62 optimal weight: 2.9990 chunk 319 optimal weight: 0.6980 chunk 321 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 215 optimal weight: 0.5980 chunk 378 optimal weight: 7.9990 chunk 190 optimal weight: 0.6980 chunk 181 optimal weight: 5.9990 chunk 281 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 70 optimal weight: 0.0040 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 93 GLN J1249 ASN K 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.132424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.076120 restraints weight = 50600.706| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.78 r_work: 0.2828 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33172 Z= 0.118 Angle : 0.547 11.499 45396 Z= 0.290 Chirality : 0.041 0.260 5198 Planarity : 0.004 0.046 5427 Dihedral : 17.945 174.886 5696 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.67 % Rotamer: Outliers : 3.67 % Allowed : 18.46 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.14), residues: 3732 helix: 1.60 (0.14), residues: 1503 sheet: -1.33 (0.25), residues: 421 loop : -1.39 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 77 TYR 0.018 0.001 TYR L 148 PHE 0.009 0.001 PHE I 505 TRP 0.011 0.001 TRP J1020 HIS 0.003 0.000 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (33164) covalent geometry : angle 0.54395 / 0.29 (45384) hydrogen bonds : bond 0.03586 / 2.43 ( 1371) hydrogen bonds : angle 3.97573 / 2.73 ( 3764) metal coordination : bond 0.00429 / 0.25 ( 8) metal coordination : angle 3.32667 / 1.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 241 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 212 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7250 (t0) REVERT: G 228 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6976 (mp) REVERT: H 66 HIS cc_start: 0.8033 (t-170) cc_final: 0.7644 (t-90) REVERT: H 75 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7537 (pm20) REVERT: H 103 ASN cc_start: 0.8885 (t0) cc_final: 0.8590 (t0) REVERT: I 276 GLN cc_start: 0.8843 (mt0) cc_final: 0.8478 (tm-30) REVERT: I 315 MET cc_start: 0.8135 (ttp) cc_final: 0.7385 (ptm) REVERT: I 332 ARG cc_start: 0.7911 (mtp85) cc_final: 0.7147 (mtp85) REVERT: I 414 ILE cc_start: 0.9389 (pt) cc_final: 0.9164 (pt) REVERT: I 524 ILE cc_start: 0.8651 (tt) cc_final: 0.8439 (tt) REVERT: I 538 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8535 (pp) REVERT: I 704 MET cc_start: 0.8027 (mmm) cc_final: 0.7685 (tpp) REVERT: I 1327 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7940 (mp) REVERT: I 1340 GLU cc_start: 0.7811 (pp20) cc_final: 0.7343 (pt0) REVERT: J 196 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7787 (tm-30) REVERT: J 197 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: J 267 ASP cc_start: 0.8198 (t70) cc_final: 0.7882 (t0) REVERT: J 497 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8216 (mm-30) REVERT: J 709 ARG cc_start: 0.7019 (ppt170) cc_final: 0.6752 (ppt170) REVERT: J 731 ARG cc_start: 0.8660 (tpt-90) cc_final: 0.8258 (tpp-160) REVERT: J 790 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7986 (p) REVERT: J 849 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7513 (pp) REVERT: J 907 HIS cc_start: 0.8077 (p90) cc_final: 0.7656 (p-80) REVERT: J 1193 TRP cc_start: 0.8744 (p90) cc_final: 0.8363 (p90) REVERT: K 43 ASN cc_start: 0.8853 (t0) cc_final: 0.8323 (t0) REVERT: L 277 MET cc_start: 0.7870 (tpt) cc_final: 0.7337 (tpp) REVERT: L 474 MET cc_start: 0.8582 (ptm) cc_final: 0.8298 (ptm) REVERT: L 476 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7791 (pmt-80) REVERT: L 507 MET cc_start: 0.8911 (ttm) cc_final: 0.8581 (tpp) REVERT: L 567 MET cc_start: 0.8235 (mtm) cc_final: 0.7893 (mtm) outliers start: 118 outliers final: 95 residues processed: 347 average time/residue: 0.1934 time to fit residues: 110.6667 Evaluate side-chains 337 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 233 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1019 ASP Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 236 LYS Chi-restraints excluded: chain L residue 353 LEU Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 609 SER Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain R residue 260 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 23 optimal weight: 6.9990 chunk 336 optimal weight: 50.0000 chunk 273 optimal weight: 5.9990 chunk 278 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 261 optimal weight: 0.4980 chunk 105 optimal weight: 10.0000 chunk 213 optimal weight: 0.5980 chunk 347 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.131290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.074896 restraints weight = 50577.825| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.77 r_work: 0.2805 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33172 Z= 0.174 Angle : 0.573 12.034 45396 Z= 0.302 Chirality : 0.042 0.264 5198 Planarity : 0.004 0.047 5427 Dihedral : 17.979 175.137 5696 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.87 % Favored : 94.08 % Rotamer: Outliers : 3.88 % Allowed : 18.30 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.14), residues: 3732 helix: 1.58 (0.14), residues: 1503 sheet: -1.33 (0.25), residues: 421 loop : -1.36 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 77 TYR 0.018 0.001 TYR J 144 PHE 0.011 0.001 PHE I 186 TRP 0.021 0.001 TRP L 326 HIS 0.004 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (33164) covalent geometry : angle 0.57085 / 0.30 (45384) hydrogen bonds : bond 0.03838 / 2.60 ( 1371) hydrogen bonds : angle 4.00726 / 2.75 ( 3764) metal coordination : bond 0.00650 / 0.39 ( 8) metal coordination : angle 3.23950 / 1.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 235 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 212 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7278 (t0) REVERT: G 228 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7008 (mp) REVERT: H 66 HIS cc_start: 0.8034 (t-170) cc_final: 0.7595 (t-90) REVERT: H 75 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: I 276 GLN cc_start: 0.8842 (mt0) cc_final: 0.8478 (tm-30) REVERT: I 315 MET cc_start: 0.8176 (ttp) cc_final: 0.7404 (ptm) REVERT: I 332 ARG cc_start: 0.7923 (mtp85) cc_final: 0.7150 (mtp85) REVERT: I 414 ILE cc_start: 0.9399 (pt) cc_final: 0.9178 (pt) REVERT: I 524 ILE cc_start: 0.8730 (tt) cc_final: 0.8504 (tt) REVERT: I 529 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7860 (mtt-85) REVERT: I 538 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8569 (pp) REVERT: I 637 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.5651 (ptm-80) REVERT: I 704 MET cc_start: 0.8138 (mmm) cc_final: 0.7831 (tpp) REVERT: I 1327 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7971 (mp) REVERT: I 1340 GLU cc_start: 0.7823 (pp20) cc_final: 0.7367 (pt0) REVERT: J 196 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7804 (tm-30) REVERT: J 197 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: J 227 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.6492 (t80) REVERT: J 267 ASP cc_start: 0.8249 (t70) cc_final: 0.7929 (t0) REVERT: J 497 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8162 (mm-30) REVERT: J 731 ARG cc_start: 0.8710 (tpt-90) cc_final: 0.8329 (tpp-160) REVERT: J 790 THR cc_start: 0.8338 (OUTLIER) cc_final: 0.8067 (p) REVERT: J 849 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7579 (pp) REVERT: J 907 HIS cc_start: 0.8082 (p90) cc_final: 0.7677 (p-80) REVERT: J 1193 TRP cc_start: 0.8736 (p90) cc_final: 0.8359 (p90) REVERT: K 43 ASN cc_start: 0.8883 (t0) cc_final: 0.8213 (t0) REVERT: L 277 MET cc_start: 0.7847 (tpt) cc_final: 0.7327 (tpp) REVERT: L 474 MET cc_start: 0.8593 (ptm) cc_final: 0.8321 (ptm) REVERT: L 476 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7775 (pmt-80) REVERT: L 507 MET cc_start: 0.8915 (ttm) cc_final: 0.8609 (tpp) REVERT: L 567 MET cc_start: 0.8243 (mtm) cc_final: 0.7939 (mtm) outliers start: 125 outliers final: 107 residues processed: 345 average time/residue: 0.1902 time to fit residues: 107.6666 Evaluate side-chains 353 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 234 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 529 ARG Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 610 GLU Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 637 ARG Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1019 ASP Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 236 LYS Chi-restraints excluded: chain L residue 353 LEU Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 609 SER Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain R residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 376 optimal weight: 40.0000 chunk 267 optimal weight: 0.5980 chunk 109 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 chunk 234 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 293 optimal weight: 20.0000 chunk 129 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 350 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 93 GLN K 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.131333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.074937 restraints weight = 50972.814| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.78 r_work: 0.2805 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33172 Z= 0.168 Angle : 0.573 11.347 45396 Z= 0.303 Chirality : 0.042 0.264 5198 Planarity : 0.004 0.047 5427 Dihedral : 17.978 175.149 5694 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.68 % Favored : 94.27 % Rotamer: Outliers : 3.98 % Allowed : 18.18 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.14), residues: 3732 helix: 1.58 (0.14), residues: 1504 sheet: -1.26 (0.25), residues: 428 loop : -1.36 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 77 TYR 0.017 0.001 TYR L 137 PHE 0.015 0.001 PHE J1199 TRP 0.017 0.001 TRP L 326 HIS 0.003 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (33164) covalent geometry : angle 0.57078 / 0.30 (45384) hydrogen bonds : bond 0.03828 / 2.59 ( 1371) hydrogen bonds : angle 4.00536 / 2.74 ( 3764) metal coordination : bond 0.00621 / 0.38 ( 8) metal coordination : angle 3.32241 / 1.85 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 241 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 212 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7287 (t0) REVERT: G 228 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7013 (mp) REVERT: H 66 HIS cc_start: 0.8032 (t-170) cc_final: 0.7597 (t-90) REVERT: H 75 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7537 (pm20) REVERT: I 145 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8511 (mp) REVERT: I 276 GLN cc_start: 0.8841 (mt0) cc_final: 0.8472 (tm-30) REVERT: I 315 MET cc_start: 0.8186 (ttp) cc_final: 0.7408 (ptm) REVERT: I 332 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7157 (mtp85) REVERT: I 524 ILE cc_start: 0.8735 (tt) cc_final: 0.8519 (tt) REVERT: I 529 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7859 (mtt-85) REVERT: I 538 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8571 (pp) REVERT: I 704 MET cc_start: 0.8138 (mmm) cc_final: 0.7803 (tpp) REVERT: I 1327 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7939 (mp) REVERT: I 1340 GLU cc_start: 0.7817 (pp20) cc_final: 0.7371 (pt0) REVERT: J 196 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7802 (tm-30) REVERT: J 197 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7005 (tt0) REVERT: J 267 ASP cc_start: 0.8262 (t70) cc_final: 0.7920 (t0) REVERT: J 497 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8169 (mm-30) REVERT: J 731 ARG cc_start: 0.8714 (tpt-90) cc_final: 0.8314 (tpp-160) REVERT: J 790 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.8070 (p) REVERT: J 849 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7581 (pp) REVERT: J 867 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8297 (mp10) REVERT: J 907 HIS cc_start: 0.8084 (p90) cc_final: 0.7677 (p-80) REVERT: J 1193 TRP cc_start: 0.8728 (p90) cc_final: 0.8352 (p90) REVERT: K 43 ASN cc_start: 0.8887 (t0) cc_final: 0.8228 (t0) REVERT: L 277 MET cc_start: 0.7815 (tpt) cc_final: 0.7302 (tpp) REVERT: L 474 MET cc_start: 0.8548 (ptm) cc_final: 0.8309 (ptm) REVERT: L 476 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7721 (pmt-80) REVERT: L 507 MET cc_start: 0.8919 (ttm) cc_final: 0.8619 (tpp) REVERT: L 567 MET cc_start: 0.8245 (mtm) cc_final: 0.7812 (mtm) outliers start: 128 outliers final: 110 residues processed: 354 average time/residue: 0.1997 time to fit residues: 116.5296 Evaluate side-chains 359 residues out of total 3220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 237 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 152 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 529 ARG Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 553 THR Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1019 ASP Chi-restraints excluded: chain I residue 1041 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 172 PHE Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 290 ILE Chi-restraints excluded: chain J residue 324 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 673 VAL Chi-restraints excluded: chain J residue 698 MET Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 867 GLN Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1307 LEU Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1357 ILE Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 236 LYS Chi-restraints excluded: chain L residue 353 LEU Chi-restraints excluded: chain L residue 457 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 609 SER Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain R residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 105 optimal weight: 7.9990 chunk 358 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 237 optimal weight: 2.9990 chunk 245 optimal weight: 9.9990 chunk 322 optimal weight: 7.9990 chunk 156 optimal weight: 0.5980 chunk 349 optimal weight: 0.9990 chunk 304 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 69 GLN I 684 ASN K 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.133409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.077238 restraints weight = 50545.041| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.79 r_work: 0.2849 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 33172 Z= 0.109 Angle : 0.543 10.913 45396 Z= 0.287 Chirality : 0.041 0.261 5198 Planarity : 0.004 0.045 5427 Dihedral : 17.837 175.175 5694 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 3.48 % Allowed : 18.89 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.14), residues: 3732 helix: 1.73 (0.14), residues: 1501 sheet: -1.15 (0.26), residues: 427 loop : -1.24 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 77 TYR 0.026 0.001 TYR L 137 PHE 0.013 0.001 PHE J1325 TRP 0.017 0.001 TRP L 326 HIS 0.003 0.000 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (33164) covalent geometry : angle 0.54040 / 0.29 (45384) hydrogen bonds : bond 0.03377 / 2.29 ( 1371) hydrogen bonds : angle 3.88429 / 2.66 ( 3764) metal coordination : bond 0.00337 / 0.19 ( 8) metal coordination : angle 3.17507 / 1.78 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8379.38 seconds wall clock time: 143 minutes 52.57 seconds (8632.57 seconds total)