Starting phenix.real_space_refine on Mon Sep 14 01:03:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f3c_28845/09_2026/8f3c_28845.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f3c_28845/09_2026/8f3c_28845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f3c_28845/09_2026/8f3c_28845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f3c_28845/09_2026/8f3c_28845.map" model { file = "/net/cci-nas-00/data/ceres_data/8f3c_28845/09_2026/8f3c_28845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f3c_28845/09_2026/8f3c_28845.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8f3c_28845/09_2026/8f3c_28845.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f3c_28845/09_2026/8f3c_28845.cif" } resolution = 3.4 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= 0.002 sd= 0.078 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: 6 Type Number sf(0) Gaussians P 94 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16490 2.51 5 N 4752 2.21 5 O 5376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.27s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26819 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 388 Inner-chain residues flagged as termini: ['pdbres=" DG A 25 "'] Classifications: {'DNA': 19} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 18} Chain: "B" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 631 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "G" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1702 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10381 Classifications: {'peptide': 1316} Link IDs: {'PTRANS': 55, 'TRANS': 1260} Chain breaks: 1 Chain: "J" Number of atoms: 10403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10403 Classifications: {'peptide': 1337} Link IDs: {'PTRANS': 55, 'TRANS': 1281} 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: "R" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 997 Classifications: {'RNAv2': 47} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 11, 'rna3p': 35} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.67, per 1000 atoms: 0.21 Number of scatterers: 26819 At special positions: 0 Unit cell: (138, 159, 163, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 106 16.00 P 94 15.00 Mg 1 11.99 O 5376 8.00 N 4752 7.00 C 16490 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: 2.16 Conformation dependent library (CDL) restraints added in 927.9 milliseconds 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 45 sheets defined 38.7% alpha, 13.8% beta 32 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 Processing helix chain 'G' and resid 77 through 88 removed outlier: 3.502A pdb=" N LEU G 88 " --> pdb=" O ASN G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 158 removed outlier: 4.116A pdb=" N ARG G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 34 through 49 removed outlier: 3.514A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.561A pdb=" N LEU H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.744A 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 154 through 158 Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'H' and resid 228 through 232 removed outlier: 4.128A pdb=" N VAL H 232 " --> pdb=" O GLU H 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 10 removed outlier: 3.685A pdb=" N ARG I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.880A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 56 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 163 through 167 removed outlier: 4.182A pdb=" N SER I 167 " --> pdb=" O THR I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.930A 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 281 Processing helix chain 'I' and resid 291 through 295 Processing helix chain 'I' and resid 318 through 329 Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.618A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.643A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 527 Processing helix chain 'I' and resid 544 through 549 removed outlier: 3.525A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.757A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 607 through 612 removed outlier: 4.010A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 662 through 667 removed outlier: 3.572A pdb=" N LEU I 667 " --> pdb=" O VAL I 663 " (cutoff:3.500A) Processing helix chain 'I' and resid 675 through 687 removed outlier: 3.655A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.849A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 738 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 865 removed outlier: 3.541A pdb=" N LEU I 862 " --> pdb=" O GLY I 858 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU I 865 " --> pdb=" O ALA I 861 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 979 Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.739A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 4.167A pdb=" N GLU I1026 " --> pdb=" O LYS I1022 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS I1027 " --> pdb=" O HIS I1023 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.667A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.637A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 removed outlier: 3.538A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.619A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1243 removed outlier: 3.821A 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 1285 through 1292 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1334 removed outlier: 3.718A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY I1334 " --> pdb=" O ILE I1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 removed outlier: 3.849A pdb=" N GLU J 171 " --> pdb=" O ASP J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 208 removed outlier: 4.402A pdb=" N GLU J 203 " --> pdb=" O GLU J 199 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU J 204 " --> pdb=" O GLN J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.659A pdb=" N SER J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix 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 309 Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.547A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (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 452 through 458 removed outlier: 4.386A pdb=" N ALA J 456 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 484 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.768A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.567A pdb=" N TRP J 580 " --> pdb=" O ARG J 576 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.669A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 Processing helix chain 'J' and resid 649 through 671 Processing helix chain 'J' and resid 674 through 703 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 4.499A pdb=" N LEU J 740 " --> pdb=" O GLN J 736 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA J 741 " --> pdb=" O ILE J 737 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.810A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 915 through 925 Processing helix chain 'J' and resid 926 through 930 Processing helix chain 'J' and resid 1137 through 1146 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 4.114A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.128A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.998A pdb=" N ASN J1295 " --> pdb=" O GLU J1291 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1313 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.673A pdb=" N SER J1324 " --> pdb=" O ILE J1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 Processing helix chain 'J' and resid 1360 through 1372 removed outlier: 4.128A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 4.074A 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 33 Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.936A pdb=" N LEU K 51 " --> pdb=" O THR K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 77 Processing helix chain 'K' and resid 78 through 80 No H-bonds generated for 'chain 'K' and resid 78 through 80' Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 17 removed outlier: 9.100A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (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 115 through 116 removed outlier: 4.366A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 91 removed outlier: 3.507A pdb=" N ARG G 91 " --> pdb=" O GLU G 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.593A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 180 through 182 removed outlier: 6.584A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 23 through 27 removed outlier: 6.543A pdb=" N LEU H 198 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA H 189 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LYS H 200 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL H 187 " --> pdb=" O LYS H 200 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL H 202 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 97 through 101 removed outlier: 3.590A pdb=" N VAL H 98 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL H 146 " --> pdb=" O VAL H 98 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN H 147 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA H 55 " --> pdb=" O GLN H 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 90 through 91 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 108 through 111 removed outlier: 3.837A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (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 'I' and resid 13 through 14 removed outlier: 6.533A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 66 through 75 removed outlier: 5.652A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET I 124 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE I 104 " --> pdb=" O ASP I 116 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB7, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AB8, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.636A pdb=" N ASN I 193 " --> pdb=" O ASP I 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AC1, first strand: chain 'I' and resid 239 through 240 removed outlier: 3.509A pdb=" N MET I 239 " --> pdb=" O ILE I 285 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.790A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 301 through 302 removed outlier: 3.564A pdb=" N CYS I 311 " --> pdb=" O TYR I 301 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.540A pdb=" N GLN I 580 " --> pdb=" O GLU I 588 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 599 through 603 removed outlier: 5.551A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.740A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AC8, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'I' and resid 1065 through 1067 removed outlier: 7.931A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET I 800 " --> pdb=" O MET I1230 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.798A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 882 through 884 removed outlier: 7.264A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD4, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AD5, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AD6, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.528A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.732A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.011A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 144 through 145 Processing sheet with id=AD8, first strand: chain 'J' and resid 350 through 356 removed outlier: 6.420A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER J 353 " --> pdb=" O MET J 466 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 547 through 556 removed outlier: 3.613A pdb=" N VAL J 550 " --> pdb=" O LYS J 570 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER J 568 " --> pdb=" O ILE J 552 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 809 through 811 removed outlier: 6.194A pdb=" N VAL J 894 " --> pdb=" O VAL J 809 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU J 811 " --> pdb=" O VAL J 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'J' and resid 825 through 826 removed outlier: 7.269A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS J 832 " --> pdb=" O VAL J 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'J' and resid 949 through 951 Processing sheet with id=AE5, first strand: chain 'J' and resid 957 through 960 removed outlier: 3.641A pdb=" N LYS J 959 " --> pdb=" O LYS J 983 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS J 983 " --> pdb=" O LYS J 959 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1034 through 1036 removed outlier: 3.531A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1059 through 1061 removed outlier: 3.593A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AE9, first strand: chain 'J' and resid 1279 through 1281 996 hydrogen bonds defined for protein. 2781 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 6.42 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7162 1.33 - 1.45: 4630 1.45 - 1.57: 15259 1.57 - 1.69: 187 1.69 - 1.81: 184 Bond restraints: 27422 Sorted by residual: bond pdb=" C1' DC A 13 " pdb=" N1 DC A 13 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.15e+01 bond pdb=" C3' DC A 13 " pdb=" C2' DC A 13 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" N GLY I 48 " pdb=" CA GLY I 48 " ideal model delta sigma weight residual 1.448 1.478 -0.030 9.20e-03 1.18e+04 1.09e+01 bond pdb=" N LEU G 31 " pdb=" CA LEU G 31 " ideal model delta sigma weight residual 1.455 1.495 -0.041 1.25e-02 6.40e+03 1.06e+01 bond pdb=" N ILE J 147 " pdb=" CA ILE J 147 " ideal model delta sigma weight residual 1.457 1.495 -0.039 1.19e-02 7.06e+03 1.05e+01 ... (remaining 27417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 36272 1.92 - 3.83: 1055 3.83 - 5.75: 118 5.75 - 7.67: 24 7.67 - 9.58: 6 Bond angle restraints: 37475 Sorted by residual: angle pdb=" N TYR J 46 " pdb=" CA TYR J 46 " pdb=" C TYR J 46 " ideal model delta sigma weight residual 112.90 105.37 7.53 1.31e+00 5.83e-01 3.30e+01 angle pdb=" C ASP J 54 " pdb=" N GLY J 55 " pdb=" CA GLY J 55 " ideal model delta sigma weight residual 122.77 116.56 6.21 1.21e+00 6.83e-01 2.63e+01 angle pdb=" C ARG J 250 " pdb=" CA ARG J 250 " pdb=" CB ARG J 250 " ideal model delta sigma weight residual 111.29 120.33 -9.04 1.92e+00 2.71e-01 2.21e+01 angle pdb=" N LEU I1291 " pdb=" CA LEU I1291 " pdb=" C LEU I1291 " ideal model delta sigma weight residual 113.61 106.59 7.02 1.50e+00 4.44e-01 2.19e+01 angle pdb=" N3 DT A 11 " pdb=" C4 DT A 11 " pdb=" O4 DT A 11 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.10e+01 ... (remaining 37470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 15938 35.89 - 71.78: 638 71.78 - 107.67: 32 107.67 - 143.56: 3 143.56 - 179.45: 2 Dihedral angle restraints: 16613 sinusoidal: 7510 harmonic: 9103 Sorted by residual: dihedral pdb=" C4' U R 24 " pdb=" C3' U R 24 " pdb=" C2' U R 24 " pdb=" C1' U R 24 " ideal model delta sinusoidal sigma weight residual 36.35 -36.33 72.67 1 3.10e+00 1.04e-01 7.01e+02 dihedral pdb=" C4' U R 26 " pdb=" C3' U R 26 " pdb=" C2' U R 26 " pdb=" C1' U R 26 " ideal model delta sinusoidal sigma weight residual 36.34 -35.53 71.88 1 3.10e+00 1.04e-01 6.88e+02 dihedral pdb=" C4' A R 16 " pdb=" C3' A R 16 " pdb=" C2' A R 16 " pdb=" C1' A R 16 " ideal model delta sinusoidal sigma weight residual 36.34 -35.52 71.86 1 3.10e+00 1.04e-01 6.88e+02 ... (remaining 16610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3913 0.092 - 0.184: 312 0.184 - 0.275: 84 0.275 - 0.367: 3 0.367 - 0.459: 5 Chirality restraints: 4317 Sorted by residual: chirality pdb=" P G R 38 " pdb=" OP1 G R 38 " pdb=" OP2 G R 38 " pdb=" O5' G R 38 " both_signs ideal model delta sigma weight residual True 2.17 -2.63 -0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" P G R 37 " pdb=" OP1 G R 37 " pdb=" OP2 G R 37 " pdb=" O5' G R 37 " both_signs ideal model delta sigma weight residual True 2.17 -2.63 -0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CG LEU J 194 " pdb=" CB LEU J 194 " pdb=" CD1 LEU J 194 " pdb=" CD2 LEU J 194 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.89e+00 ... (remaining 4314 not shown) Planarity restraints: 4556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN I 36 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C GLN I 36 " -0.077 2.00e-02 2.50e+03 pdb=" O GLN I 36 " 0.029 2.00e-02 2.50e+03 pdb=" N LYS I 37 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE J 44 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C ILE J 44 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE J 44 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN J 45 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 802 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.80e+00 pdb=" CG ASP J 802 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP J 802 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP J 802 " 0.018 2.00e-02 2.50e+03 ... (remaining 4553 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 308 2.60 - 3.18: 23128 3.18 - 3.75: 43768 3.75 - 4.33: 59012 4.33 - 4.90: 96608 Nonbonded interactions: 222824 Sorted by model distance: nonbonded pdb=" OD1 ASN I1108 " pdb=" NE2 GLN I1111 " model vdw 2.029 3.120 nonbonded pdb=" CB ASP J 460 " pdb="MG MG J1501 " model vdw 2.103 2.570 nonbonded pdb=" O ARG G 45 " pdb=" OG SER G 49 " model vdw 2.196 3.040 nonbonded pdb=" OD2 ASP I 160 " pdb=" OG1 THR I 164 " model vdw 2.207 3.040 nonbonded pdb=" O2' G R 6 " pdb=" O2' A R 27 " model vdw 2.208 3.040 ... (remaining 222819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 234)) selection = (chain 'H' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 234)) } 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: 1.950 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: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 27.710 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 27422 Z= 0.279 Angle : 0.701 9.583 37475 Z= 0.425 Chirality : 0.058 0.459 4317 Planarity : 0.004 0.093 4556 Dihedral : 17.565 179.451 10757 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.19 % Favored : 95.75 % Rotamer: Outliers : 1.15 % Allowed : 1.11 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 3152 helix: 1.19 (0.16), residues: 1081 sheet: -0.35 (0.29), residues: 322 loop : -0.66 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 156 TYR 0.026 0.001 TYR J 144 PHE 0.048 0.001 PHE I1265 TRP 0.006 0.001 TRP J 580 HIS 0.002 0.000 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.28 (27422) covalent geometry : angle 0.70089 / 0.42 (37475) hydrogen bonds : bond 0.17338 / 19.44 ( 1077) hydrogen bonds : angle 6.81496 / 7.14 ( 2939) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 475 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: G 120 ASP cc_start: 0.7883 (p0) cc_final: 0.7337 (p0) REVERT: G 176 CYS cc_start: 0.7261 (t) cc_final: 0.7049 (p) REVERT: H 71 LYS cc_start: 0.8827 (mmmm) cc_final: 0.8577 (mtmt) REVERT: H 185 TYR cc_start: 0.8282 (p90) cc_final: 0.8009 (p90) REVERT: H 192 VAL cc_start: 0.6340 (OUTLIER) cc_final: 0.6135 (p) REVERT: I 47 TYR cc_start: 0.3409 (m-10) cc_final: 0.2278 (m-10) REVERT: I 496 LYS cc_start: 0.8125 (tttt) cc_final: 0.7534 (mppt) REVERT: I 1080 ASN cc_start: 0.8697 (t0) cc_final: 0.8380 (t0) REVERT: J 136 GLU cc_start: 0.8186 (pp20) cc_final: 0.6834 (tp30) REVERT: J 140 TYR cc_start: 0.7601 (m-10) cc_final: 0.6706 (m-10) REVERT: J 440 VAL cc_start: 0.9287 (t) cc_final: 0.9083 (p) REVERT: J 458 ASN cc_start: 0.8489 (t0) cc_final: 0.8270 (t0) REVERT: J 698 MET cc_start: 0.8625 (mmm) cc_final: 0.8362 (mmm) REVERT: J 992 LYS cc_start: 0.8486 (mmmt) cc_final: 0.7772 (mtpp) REVERT: J 1349 GLU cc_start: 0.7684 (mp0) cc_final: 0.7441 (mp0) REVERT: K 11 GLU cc_start: 0.7400 (mp0) cc_final: 0.7120 (mp0) REVERT: K 71 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7730 (mm-30) outliers start: 31 outliers final: 2 residues processed: 487 average time/residue: 0.1948 time to fit residues: 145.2154 Evaluate side-chains 319 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 316 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain J residue 120 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.0270 chunk 298 optimal weight: 3.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 41 ASN ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 435 GLN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.156620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.111748 restraints weight = 42332.802| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.75 r_work: 0.3204 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27422 Z= 0.185 Angle : 0.814 21.623 37475 Z= 0.380 Chirality : 0.069 1.196 4317 Planarity : 0.005 0.089 4556 Dihedral : 15.043 176.908 4566 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 1.33 % Allowed : 11.41 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 3152 helix: 1.16 (0.16), residues: 1100 sheet: -0.68 (0.28), residues: 323 loop : -0.76 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 3 TYR 0.029 0.001 TYR H 177 PHE 0.031 0.002 PHE I1025 TRP 0.007 0.001 TRP J 580 HIS 0.006 0.001 HIS H 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (27422) covalent geometry : angle 0.81423 / 0.38 (37475) hydrogen bonds : bond 0.04340 / 4.78 ( 1077) hydrogen bonds : angle 5.45012 / 5.81 ( 2939) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 363 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 141 SER cc_start: 0.8613 (m) cc_final: 0.8277 (p) REVERT: G 176 CYS cc_start: 0.8397 (t) cc_final: 0.7450 (p) REVERT: H 71 LYS cc_start: 0.8915 (mmmm) cc_final: 0.8581 (mtmt) REVERT: H 185 TYR cc_start: 0.8667 (p90) cc_final: 0.8250 (p90) REVERT: H 191 ARG cc_start: 0.7960 (ppt170) cc_final: 0.7749 (ppt170) REVERT: H 197 ASP cc_start: 0.7033 (p0) cc_final: 0.6806 (p0) REVERT: I 47 TYR cc_start: 0.2816 (m-80) cc_final: 0.2198 (m-10) REVERT: I 124 MET cc_start: 0.8232 (ptt) cc_final: 0.7978 (ppp) REVERT: I 239 MET cc_start: 0.4863 (tmm) cc_final: 0.4571 (tmm) REVERT: I 443 ASP cc_start: 0.7898 (p0) cc_final: 0.7632 (p0) REVERT: I 496 LYS cc_start: 0.8166 (tttt) cc_final: 0.7380 (mppt) REVERT: I 1061 GLN cc_start: 0.8518 (tt0) cc_final: 0.8265 (tt0) REVERT: I 1080 ASN cc_start: 0.9054 (t0) cc_final: 0.8847 (t0) REVERT: I 1188 ASP cc_start: 0.9220 (p0) cc_final: 0.8936 (p0) REVERT: J 96 LYS cc_start: 0.8476 (ptpt) cc_final: 0.7930 (pptt) REVERT: J 136 GLU cc_start: 0.8130 (pp20) cc_final: 0.6852 (tp30) REVERT: J 140 TYR cc_start: 0.7620 (m-10) cc_final: 0.7006 (m-10) REVERT: J 330 MET cc_start: 0.8272 (ptp) cc_final: 0.7984 (ptm) REVERT: J 418 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7916 (mm-30) REVERT: J 458 ASN cc_start: 0.8781 (t0) cc_final: 0.8337 (t0) REVERT: J 822 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7697 (mmm) REVERT: J 833 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7495 (mt-10) REVERT: J 847 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7835 (m-30) REVERT: J 992 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7463 (mtpp) REVERT: J 1174 ARG cc_start: 0.8082 (ptt-90) cc_final: 0.7693 (ttp80) REVERT: J 1195 GLN cc_start: 0.6845 (mt0) cc_final: 0.6237 (mp10) REVERT: J 1197 ASN cc_start: 0.7562 (p0) cc_final: 0.6764 (t0) REVERT: K 11 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: K 70 GLN cc_start: 0.7509 (tm-30) cc_final: 0.7288 (mm-40) outliers start: 36 outliers final: 18 residues processed: 379 average time/residue: 0.1697 time to fit residues: 103.2981 Evaluate side-chains 326 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 305 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 602 SER Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 955 LYS Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 194 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 266 optimal weight: 6.9990 chunk 258 optimal weight: 10.0000 chunk 301 optimal weight: 9.9990 chunk 45 optimal weight: 0.4980 chunk 221 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 488 ASN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 ASN J 736 GLN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.153608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.109779 restraints weight = 41741.903| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.67 r_work: 0.3201 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27422 Z= 0.148 Angle : 0.658 10.661 37475 Z= 0.321 Chirality : 0.053 0.810 4317 Planarity : 0.004 0.045 4556 Dihedral : 14.948 177.660 4563 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.78 % Allowed : 14.93 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.15), residues: 3152 helix: 1.16 (0.16), residues: 1108 sheet: -0.64 (0.28), residues: 327 loop : -0.72 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 322 TYR 0.024 0.001 TYR H 177 PHE 0.038 0.001 PHE I1025 TRP 0.013 0.001 TRP J 115 HIS 0.005 0.001 HIS H 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (27422) covalent geometry : angle 0.65836 / 0.32 (37475) hydrogen bonds : bond 0.03996 / 4.36 ( 1077) hydrogen bonds : angle 5.13367 / 5.53 ( 2939) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 329 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 176 CYS cc_start: 0.8413 (t) cc_final: 0.7476 (p) REVERT: H 71 LYS cc_start: 0.8876 (mmmm) cc_final: 0.8653 (mtmt) REVERT: H 185 TYR cc_start: 0.8648 (p90) cc_final: 0.8208 (p90) REVERT: H 197 ASP cc_start: 0.7237 (p0) cc_final: 0.7008 (p0) REVERT: I 47 TYR cc_start: 0.3065 (m-80) cc_final: 0.2511 (m-10) REVERT: I 124 MET cc_start: 0.8304 (ptt) cc_final: 0.7931 (ppp) REVERT: I 239 MET cc_start: 0.4914 (tmm) cc_final: 0.4459 (tmm) REVERT: I 443 ASP cc_start: 0.8013 (p0) cc_final: 0.7689 (p0) REVERT: I 496 LYS cc_start: 0.8161 (tttt) cc_final: 0.7374 (mppt) REVERT: I 510 GLN cc_start: 0.8434 (tp-100) cc_final: 0.8161 (tp-100) REVERT: I 637 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7784 (ttp80) REVERT: I 697 LYS cc_start: 0.8492 (pptt) cc_final: 0.7489 (pptt) REVERT: I 781 ASP cc_start: 0.8122 (t0) cc_final: 0.7808 (t0) REVERT: I 1188 ASP cc_start: 0.9302 (p0) cc_final: 0.8953 (p0) REVERT: I 1233 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8867 (mt) REVERT: J 52 GLU cc_start: 0.7037 (tp30) cc_final: 0.6549 (mm-30) REVERT: J 96 LYS cc_start: 0.8481 (ptpt) cc_final: 0.7905 (pptt) REVERT: J 136 GLU cc_start: 0.8210 (pp20) cc_final: 0.6911 (tp30) REVERT: J 140 TYR cc_start: 0.7775 (m-10) cc_final: 0.7036 (m-10) REVERT: J 186 GLN cc_start: 0.8318 (tt0) cc_final: 0.7991 (tt0) REVERT: J 238 ILE cc_start: 0.9012 (mm) cc_final: 0.8677 (mm) REVERT: J 343 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8638 (mm) REVERT: J 418 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7964 (mm-30) REVERT: J 833 GLU cc_start: 0.7952 (mt-10) cc_final: 0.6891 (mt-10) REVERT: J 847 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: J 983 LYS cc_start: 0.8023 (pttm) cc_final: 0.7805 (pttm) REVERT: J 992 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7521 (mtpp) REVERT: J 1146 GLU cc_start: 0.8391 (tt0) cc_final: 0.8055 (tt0) REVERT: J 1174 ARG cc_start: 0.8195 (ptt-90) cc_final: 0.7800 (ttp80) REVERT: J 1195 GLN cc_start: 0.6902 (mt0) cc_final: 0.6289 (mp10) REVERT: J 1197 ASN cc_start: 0.7560 (p0) cc_final: 0.6761 (t0) REVERT: J 1278 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7537 (pt0) REVERT: K 11 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: K 63 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.7042 (mp) REVERT: K 70 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7404 (mm-40) outliers start: 48 outliers final: 30 residues processed: 360 average time/residue: 0.1787 time to fit residues: 103.2409 Evaluate side-chains 338 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 303 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 642 SER Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 759 SER Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 602 SER Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 955 LYS Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 230 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 206 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 189 optimal weight: 0.9980 chunk 223 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 23 HIS ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 517 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.157883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.114176 restraints weight = 41637.261| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.59 r_work: 0.3210 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27422 Z= 0.135 Angle : 0.622 11.113 37475 Z= 0.303 Chirality : 0.050 0.493 4317 Planarity : 0.004 0.044 4556 Dihedral : 14.802 176.991 4561 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.85 % Allowed : 17.38 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.15), residues: 3152 helix: 1.24 (0.16), residues: 1109 sheet: -0.63 (0.29), residues: 314 loop : -0.68 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 3 TYR 0.021 0.001 TYR I1229 PHE 0.029 0.001 PHE I1025 TRP 0.025 0.001 TRP J 115 HIS 0.004 0.001 HIS H 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (27422) covalent geometry : angle 0.62222 / 0.30 (37475) hydrogen bonds : bond 0.03630 / 3.97 ( 1077) hydrogen bonds : angle 4.97837 / 5.41 ( 2939) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 322 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: H 46 ILE cc_start: 0.8900 (tp) cc_final: 0.8567 (tp) REVERT: H 71 LYS cc_start: 0.8868 (mmmm) cc_final: 0.8621 (mtmt) REVERT: H 185 TYR cc_start: 0.8633 (p90) cc_final: 0.8208 (p90) REVERT: H 197 ASP cc_start: 0.7376 (p0) cc_final: 0.7114 (p0) REVERT: I 47 TYR cc_start: 0.2918 (m-80) cc_final: 0.2419 (m-10) REVERT: I 124 MET cc_start: 0.8263 (ptt) cc_final: 0.7874 (ppp) REVERT: I 443 ASP cc_start: 0.7993 (p0) cc_final: 0.7624 (p0) REVERT: I 496 LYS cc_start: 0.8178 (tttt) cc_final: 0.7399 (mppt) REVERT: I 697 LYS cc_start: 0.8559 (pptt) cc_final: 0.7629 (pptt) REVERT: I 781 ASP cc_start: 0.8212 (t0) cc_final: 0.7835 (t0) REVERT: I 1188 ASP cc_start: 0.9290 (p0) cc_final: 0.8937 (p0) REVERT: I 1233 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8853 (mt) REVERT: J 52 GLU cc_start: 0.7103 (tp30) cc_final: 0.6594 (mm-30) REVERT: J 96 LYS cc_start: 0.8467 (ptpt) cc_final: 0.7896 (pptt) REVERT: J 136 GLU cc_start: 0.8196 (pp20) cc_final: 0.7003 (tp30) REVERT: J 140 TYR cc_start: 0.7771 (m-10) cc_final: 0.7038 (m-10) REVERT: J 180 MET cc_start: 0.7992 (tmm) cc_final: 0.7690 (tmm) REVERT: J 343 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8634 (mm) REVERT: J 418 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8013 (mm-30) REVERT: J 833 GLU cc_start: 0.7968 (mt-10) cc_final: 0.6903 (mt-10) REVERT: J 847 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: J 959 LYS cc_start: 0.8523 (pttt) cc_final: 0.8315 (pttt) REVERT: J 983 LYS cc_start: 0.8043 (pttm) cc_final: 0.7486 (pttm) REVERT: J 992 LYS cc_start: 0.8194 (mmmt) cc_final: 0.7523 (mtpp) REVERT: J 1040 MET cc_start: 0.5782 (mpp) cc_final: 0.5542 (mpp) REVERT: J 1174 ARG cc_start: 0.8251 (ptt-90) cc_final: 0.7827 (ttp80) REVERT: J 1195 GLN cc_start: 0.6904 (mt0) cc_final: 0.6261 (mp10) REVERT: J 1197 ASN cc_start: 0.7570 (p0) cc_final: 0.6687 (t0) REVERT: J 1278 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7514 (pt0) REVERT: K 11 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: K 63 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7130 (mp) outliers start: 50 outliers final: 29 residues processed: 354 average time/residue: 0.1792 time to fit residues: 101.5936 Evaluate side-chains 332 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 298 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 260 PHE Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 602 SER Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 955 LYS Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 153 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 31 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 307 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 120 optimal weight: 0.0170 chunk 248 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.156732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113881 restraints weight = 42079.321| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.59 r_work: 0.3220 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27422 Z= 0.129 Angle : 0.605 9.452 37475 Z= 0.297 Chirality : 0.048 0.393 4317 Planarity : 0.004 0.044 4556 Dihedral : 14.773 176.216 4561 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.26 % Allowed : 18.27 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.15), residues: 3152 helix: 1.30 (0.16), residues: 1108 sheet: -0.61 (0.28), residues: 332 loop : -0.68 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 322 TYR 0.023 0.001 TYR I1229 PHE 0.032 0.001 PHE I1025 TRP 0.030 0.001 TRP J 115 HIS 0.003 0.001 HIS H 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (27422) covalent geometry : angle 0.60524 / 0.30 (37475) hydrogen bonds : bond 0.03524 / 3.85 ( 1077) hydrogen bonds : angle 4.85172 / 5.29 ( 2939) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 316 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.8228 (m-80) cc_final: 0.8001 (m-80) REVERT: H 46 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8732 (tp) REVERT: H 71 LYS cc_start: 0.8876 (mmmm) cc_final: 0.8605 (mtmt) REVERT: H 185 TYR cc_start: 0.8761 (p90) cc_final: 0.8302 (p90) REVERT: H 197 ASP cc_start: 0.7743 (p0) cc_final: 0.7409 (p0) REVERT: I 47 TYR cc_start: 0.3147 (m-10) cc_final: 0.2593 (m-10) REVERT: I 237 LEU cc_start: 0.7120 (tp) cc_final: 0.6872 (pp) REVERT: I 443 ASP cc_start: 0.8124 (p0) cc_final: 0.7719 (p0) REVERT: I 496 LYS cc_start: 0.8169 (tttt) cc_final: 0.7353 (mppt) REVERT: I 546 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8008 (mp0) REVERT: I 697 LYS cc_start: 0.8640 (pptt) cc_final: 0.7815 (pptt) REVERT: I 781 ASP cc_start: 0.8294 (t0) cc_final: 0.7894 (t0) REVERT: I 798 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7923 (mt0) REVERT: I 1188 ASP cc_start: 0.9349 (p0) cc_final: 0.8995 (p0) REVERT: I 1233 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8921 (mt) REVERT: J 52 GLU cc_start: 0.7207 (tp30) cc_final: 0.6761 (mm-30) REVERT: J 69 GLU cc_start: 0.7636 (mp0) cc_final: 0.7246 (mp0) REVERT: J 96 LYS cc_start: 0.8536 (ptpt) cc_final: 0.7964 (pptt) REVERT: J 136 GLU cc_start: 0.8306 (pp20) cc_final: 0.7238 (tp30) REVERT: J 140 TYR cc_start: 0.7815 (m-10) cc_final: 0.6978 (m-10) REVERT: J 180 MET cc_start: 0.8024 (tmm) cc_final: 0.7706 (tmm) REVERT: J 186 GLN cc_start: 0.8119 (tt0) cc_final: 0.7553 (tt0) REVERT: J 343 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8667 (mm) REVERT: J 747 MET cc_start: 0.8290 (mtp) cc_final: 0.8018 (mtp) REVERT: J 847 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7790 (m-30) REVERT: J 959 LYS cc_start: 0.8511 (pttt) cc_final: 0.8296 (pttt) REVERT: J 992 LYS cc_start: 0.8212 (mmmt) cc_final: 0.7548 (mtpp) REVERT: J 1040 MET cc_start: 0.5971 (mpp) cc_final: 0.5698 (mpp) REVERT: J 1174 ARG cc_start: 0.8303 (ptt-90) cc_final: 0.8069 (ttp80) REVERT: J 1195 GLN cc_start: 0.7044 (mt0) cc_final: 0.6370 (mp10) REVERT: J 1197 ASN cc_start: 0.7498 (p0) cc_final: 0.6631 (t0) REVERT: J 1278 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7547 (pt0) REVERT: K 11 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: K 63 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7194 (mp) REVERT: K 70 GLN cc_start: 0.8235 (mm-40) cc_final: 0.8022 (mm-40) outliers start: 61 outliers final: 37 residues processed: 359 average time/residue: 0.1722 time to fit residues: 100.1947 Evaluate side-chains 339 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 295 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 798 GLN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 602 SER Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 955 LYS Chi-restraints excluded: chain J residue 1314 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 282 optimal weight: 30.0000 chunk 167 optimal weight: 0.9980 chunk 292 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 279 optimal weight: 30.0000 chunk 190 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.154395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108578 restraints weight = 42063.008| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.47 r_work: 0.3175 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27422 Z= 0.169 Angle : 0.622 17.591 37475 Z= 0.305 Chirality : 0.048 0.348 4317 Planarity : 0.004 0.044 4556 Dihedral : 14.800 175.468 4561 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.26 % Allowed : 19.41 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 3152 helix: 1.28 (0.16), residues: 1111 sheet: -0.64 (0.28), residues: 324 loop : -0.69 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 3 TYR 0.025 0.001 TYR I1229 PHE 0.034 0.001 PHE I1025 TRP 0.037 0.001 TRP J 115 HIS 0.004 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (27422) covalent geometry : angle 0.62215 / 0.30 (37475) hydrogen bonds : bond 0.03562 / 3.90 ( 1077) hydrogen bonds : angle 4.84015 / 5.29 ( 2939) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 312 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.8259 (m-80) cc_final: 0.8018 (m-80) REVERT: H 46 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8713 (tp) REVERT: H 71 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8633 (mtmt) REVERT: H 185 TYR cc_start: 0.8749 (p90) cc_final: 0.8301 (p90) REVERT: H 197 ASP cc_start: 0.7579 (p0) cc_final: 0.7274 (p0) REVERT: I 47 TYR cc_start: 0.2900 (m-10) cc_final: 0.2461 (m-10) REVERT: I 124 MET cc_start: 0.8067 (ptt) cc_final: 0.7768 (ppp) REVERT: I 237 LEU cc_start: 0.7085 (tp) cc_final: 0.6829 (pp) REVERT: I 239 MET cc_start: 0.5070 (tmm) cc_final: 0.4745 (tmm) REVERT: I 443 ASP cc_start: 0.8029 (p0) cc_final: 0.7652 (p0) REVERT: I 496 LYS cc_start: 0.8227 (tttt) cc_final: 0.7408 (mppt) REVERT: I 569 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9158 (tp) REVERT: I 781 ASP cc_start: 0.8302 (t0) cc_final: 0.7879 (t0) REVERT: I 798 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8123 (mt0) REVERT: I 1188 ASP cc_start: 0.9328 (p0) cc_final: 0.8979 (p0) REVERT: I 1233 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8831 (mt) REVERT: J 52 GLU cc_start: 0.7227 (tp30) cc_final: 0.6803 (mm-30) REVERT: J 53 ARG cc_start: 0.8343 (tmt170) cc_final: 0.8090 (tpt90) REVERT: J 69 GLU cc_start: 0.7620 (mp0) cc_final: 0.7386 (mp0) REVERT: J 96 LYS cc_start: 0.8429 (ptpt) cc_final: 0.7875 (pptt) REVERT: J 136 GLU cc_start: 0.8152 (pp20) cc_final: 0.7159 (tp30) REVERT: J 140 TYR cc_start: 0.7824 (m-10) cc_final: 0.6959 (m-10) REVERT: J 180 MET cc_start: 0.8114 (tmm) cc_final: 0.7759 (tmm) REVERT: J 186 GLN cc_start: 0.8042 (tt0) cc_final: 0.7507 (tt0) REVERT: J 343 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8635 (mm) REVERT: J 375 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7617 (tp30) REVERT: J 747 MET cc_start: 0.8056 (mtp) cc_final: 0.7809 (mtp) REVERT: J 833 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7034 (mt-10) REVERT: J 847 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: J 992 LYS cc_start: 0.8195 (mmmt) cc_final: 0.7543 (mtpp) REVERT: J 1040 MET cc_start: 0.5912 (mpp) cc_final: 0.5645 (mpp) REVERT: J 1174 ARG cc_start: 0.8318 (ptt-90) cc_final: 0.8083 (ttp80) REVERT: J 1195 GLN cc_start: 0.7121 (mt0) cc_final: 0.6441 (mp10) REVERT: J 1197 ASN cc_start: 0.7402 (p0) cc_final: 0.6634 (t0) REVERT: J 1278 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7554 (pt0) REVERT: K 11 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: K 70 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7983 (mm-40) outliers start: 61 outliers final: 45 residues processed: 355 average time/residue: 0.1739 time to fit residues: 99.1750 Evaluate side-chains 340 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 288 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 798 GLN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 602 SER Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 955 LYS Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 61 optimal weight: 0.8980 chunk 304 optimal weight: 0.0870 chunk 301 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 chunk 277 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 285 optimal weight: 5.9990 chunk 279 optimal weight: 30.0000 chunk 189 optimal weight: 0.6980 chunk 233 optimal weight: 6.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.156342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112843 restraints weight = 41958.330| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.66 r_work: 0.3204 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27422 Z= 0.124 Angle : 0.604 15.501 37475 Z= 0.295 Chirality : 0.047 0.340 4317 Planarity : 0.004 0.043 4556 Dihedral : 14.768 175.023 4561 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.22 % Allowed : 20.49 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.15), residues: 3152 helix: 1.32 (0.16), residues: 1111 sheet: -0.56 (0.29), residues: 318 loop : -0.68 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 202 TYR 0.023 0.001 TYR I1229 PHE 0.034 0.001 PHE I1025 TRP 0.039 0.001 TRP J 115 HIS 0.003 0.001 HIS H 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (27422) covalent geometry : angle 0.60393 / 0.30 (37475) hydrogen bonds : bond 0.03402 / 3.72 ( 1077) hydrogen bonds : angle 4.75610 / 5.21 ( 2939) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 315 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8702 (tp) REVERT: H 71 LYS cc_start: 0.8892 (mmmm) cc_final: 0.8641 (mtmt) REVERT: H 185 TYR cc_start: 0.8710 (p90) cc_final: 0.8267 (p90) REVERT: H 197 ASP cc_start: 0.7661 (p0) cc_final: 0.7324 (p0) REVERT: I 47 TYR cc_start: 0.2929 (m-10) cc_final: 0.1078 (m-10) REVERT: I 124 MET cc_start: 0.8006 (ptt) cc_final: 0.7747 (ppp) REVERT: I 237 LEU cc_start: 0.7198 (tp) cc_final: 0.6889 (pp) REVERT: I 239 MET cc_start: 0.5227 (tmm) cc_final: 0.4895 (tmm) REVERT: I 443 ASP cc_start: 0.8014 (p0) cc_final: 0.7625 (p0) REVERT: I 496 LYS cc_start: 0.8239 (tttt) cc_final: 0.7419 (mppt) REVERT: I 510 GLN cc_start: 0.8686 (tp-100) cc_final: 0.8423 (tp-100) REVERT: I 546 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7898 (mp0) REVERT: I 781 ASP cc_start: 0.8249 (t0) cc_final: 0.7827 (t0) REVERT: I 798 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8096 (mt0) REVERT: I 1188 ASP cc_start: 0.9293 (p0) cc_final: 0.8966 (p0) REVERT: I 1233 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8801 (mt) REVERT: J 52 GLU cc_start: 0.7174 (tp30) cc_final: 0.6750 (mm-30) REVERT: J 53 ARG cc_start: 0.8332 (tmt170) cc_final: 0.8077 (tmt170) REVERT: J 69 GLU cc_start: 0.7608 (mp0) cc_final: 0.7328 (mp0) REVERT: J 96 LYS cc_start: 0.8393 (ptpt) cc_final: 0.7838 (pptt) REVERT: J 136 GLU cc_start: 0.8207 (pp20) cc_final: 0.7263 (tp30) REVERT: J 140 TYR cc_start: 0.7834 (m-10) cc_final: 0.6962 (m-10) REVERT: J 180 MET cc_start: 0.8109 (tmm) cc_final: 0.7771 (tmm) REVERT: J 322 ARG cc_start: 0.7684 (mtm110) cc_final: 0.7194 (mtm180) REVERT: J 343 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8616 (mm) REVERT: J 375 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7682 (tp30) REVERT: J 460 ASP cc_start: 0.8145 (m-30) cc_final: 0.7937 (m-30) REVERT: J 478 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8330 (tp) REVERT: J 847 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: J 932 MET cc_start: 0.7739 (mmt) cc_final: 0.7453 (mmt) REVERT: J 992 LYS cc_start: 0.8168 (mmmt) cc_final: 0.7511 (mtpp) REVERT: J 1040 MET cc_start: 0.5895 (mpp) cc_final: 0.5590 (mpp) REVERT: J 1174 ARG cc_start: 0.8321 (ptt-90) cc_final: 0.8065 (ttp80) REVERT: J 1195 GLN cc_start: 0.7084 (mt0) cc_final: 0.6387 (mp10) REVERT: J 1197 ASN cc_start: 0.7389 (p0) cc_final: 0.6605 (t0) REVERT: K 11 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: K 70 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7994 (mm-40) outliers start: 60 outliers final: 40 residues processed: 357 average time/residue: 0.1776 time to fit residues: 102.4956 Evaluate side-chains 347 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 300 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 759 SER Chi-restraints excluded: chain I residue 798 GLN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 602 SER Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 955 LYS Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 2 optimal weight: 10.0000 chunk 302 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 251 optimal weight: 0.4980 chunk 241 optimal weight: 2.9990 chunk 308 optimal weight: 0.9980 chunk 265 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 462 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.153235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.107162 restraints weight = 42252.699| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.49 r_work: 0.3152 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27422 Z= 0.179 Angle : 0.627 14.623 37475 Z= 0.309 Chirality : 0.048 0.351 4317 Planarity : 0.004 0.049 4556 Dihedral : 14.796 175.084 4561 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.60 % Favored : 95.37 % Rotamer: Outliers : 2.59 % Allowed : 20.23 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 3152 helix: 1.30 (0.16), residues: 1104 sheet: -0.79 (0.27), residues: 349 loop : -0.66 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 202 TYR 0.024 0.001 TYR I1229 PHE 0.035 0.002 PHE I1025 TRP 0.042 0.002 TRP J 115 HIS 0.004 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (27422) covalent geometry : angle 0.62687 / 0.31 (37475) hydrogen bonds : bond 0.03551 / 3.90 ( 1077) hydrogen bonds : angle 4.78300 / 5.23 ( 2939) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 305 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: H 46 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8749 (tp) REVERT: H 71 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8634 (mtmt) REVERT: H 185 TYR cc_start: 0.8814 (p90) cc_final: 0.8372 (p90) REVERT: H 197 ASP cc_start: 0.7787 (p0) cc_final: 0.7471 (p0) REVERT: I 47 TYR cc_start: 0.3087 (m-10) cc_final: 0.1124 (m-10) REVERT: I 237 LEU cc_start: 0.7228 (tp) cc_final: 0.6769 (pp) REVERT: I 239 MET cc_start: 0.5320 (tmm) cc_final: 0.4922 (tmm) REVERT: I 443 ASP cc_start: 0.8125 (p0) cc_final: 0.7732 (p0) REVERT: I 496 LYS cc_start: 0.8242 (tttt) cc_final: 0.7440 (mppt) REVERT: I 510 GLN cc_start: 0.8816 (tp-100) cc_final: 0.8515 (tp-100) REVERT: I 569 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8979 (tp) REVERT: I 781 ASP cc_start: 0.8289 (t0) cc_final: 0.7850 (t0) REVERT: I 1034 ARG cc_start: 0.8289 (mmp80) cc_final: 0.8081 (mmp80) REVERT: I 1188 ASP cc_start: 0.9342 (p0) cc_final: 0.8940 (p0) REVERT: I 1233 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8822 (mt) REVERT: J 52 GLU cc_start: 0.7267 (tp30) cc_final: 0.6869 (mm-30) REVERT: J 53 ARG cc_start: 0.8304 (tmt170) cc_final: 0.8048 (tmt170) REVERT: J 69 GLU cc_start: 0.7647 (mp0) cc_final: 0.7293 (mp0) REVERT: J 96 LYS cc_start: 0.8421 (ptpt) cc_final: 0.7874 (pptt) REVERT: J 129 ASP cc_start: 0.7835 (t0) cc_final: 0.7400 (t0) REVERT: J 136 GLU cc_start: 0.8128 (pp20) cc_final: 0.7255 (tp30) REVERT: J 140 TYR cc_start: 0.7827 (m-10) cc_final: 0.7072 (m-10) REVERT: J 144 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7334 (m-10) REVERT: J 180 MET cc_start: 0.8069 (tmm) cc_final: 0.7634 (tmm) REVERT: J 186 GLN cc_start: 0.8079 (tt0) cc_final: 0.7659 (tt0) REVERT: J 237 MET cc_start: 0.9060 (mtt) cc_final: 0.8797 (mtt) REVERT: J 322 ARG cc_start: 0.7674 (mtm110) cc_final: 0.7188 (mtm180) REVERT: J 343 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8676 (mm) REVERT: J 375 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7667 (tp30) REVERT: J 457 TYR cc_start: 0.8664 (m-80) cc_final: 0.8348 (m-80) REVERT: J 460 ASP cc_start: 0.8248 (m-30) cc_final: 0.8009 (m-30) REVERT: J 747 MET cc_start: 0.7816 (mtp) cc_final: 0.7529 (mtp) REVERT: J 770 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8235 (mt) REVERT: J 847 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7540 (m-30) REVERT: J 932 MET cc_start: 0.7808 (mmt) cc_final: 0.7498 (mmt) REVERT: J 992 LYS cc_start: 0.8161 (mmmt) cc_final: 0.7516 (mtpp) REVERT: J 1040 MET cc_start: 0.5890 (mpp) cc_final: 0.5584 (mpp) REVERT: J 1195 GLN cc_start: 0.7301 (mt0) cc_final: 0.6638 (mp10) REVERT: J 1197 ASN cc_start: 0.7508 (p0) cc_final: 0.6593 (t0) REVERT: K 11 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7321 (mp0) outliers start: 70 outliers final: 50 residues processed: 361 average time/residue: 0.1752 time to fit residues: 101.4013 Evaluate side-chains 348 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 290 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 759 SER Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 144 TYR Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 602 SER Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 282 optimal weight: 0.3980 chunk 185 optimal weight: 8.9990 chunk 214 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 314 optimal weight: 0.9980 chunk 302 optimal weight: 0.1980 chunk 316 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.157075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.114301 restraints weight = 41602.954| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.53 r_work: 0.3196 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27422 Z= 0.126 Angle : 0.606 14.349 37475 Z= 0.298 Chirality : 0.047 0.339 4317 Planarity : 0.004 0.043 4556 Dihedral : 14.767 174.346 4561 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.62 % Rotamer: Outliers : 2.33 % Allowed : 20.90 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.15), residues: 3152 helix: 1.35 (0.16), residues: 1103 sheet: -0.64 (0.28), residues: 330 loop : -0.65 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 202 TYR 0.023 0.001 TYR I1229 PHE 0.048 0.001 PHE I1025 TRP 0.043 0.001 TRP J 115 HIS 0.003 0.001 HIS G 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (27422) covalent geometry : angle 0.60604 / 0.30 (37475) hydrogen bonds : bond 0.03379 / 3.70 ( 1077) hydrogen bonds : angle 4.74391 / 5.19 ( 2939) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 307 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.8266 (m-80) cc_final: 0.7867 (t80) REVERT: H 71 LYS cc_start: 0.8904 (mmmm) cc_final: 0.8641 (mtmt) REVERT: H 185 TYR cc_start: 0.8738 (p90) cc_final: 0.8306 (p90) REVERT: H 197 ASP cc_start: 0.7707 (p0) cc_final: 0.7421 (p0) REVERT: I 47 TYR cc_start: 0.3031 (m-10) cc_final: 0.1115 (m-80) REVERT: I 237 LEU cc_start: 0.7381 (tp) cc_final: 0.6933 (pp) REVERT: I 239 MET cc_start: 0.5325 (tmm) cc_final: 0.4916 (tmm) REVERT: I 443 ASP cc_start: 0.8032 (p0) cc_final: 0.7645 (p0) REVERT: I 496 LYS cc_start: 0.8231 (tttt) cc_final: 0.7439 (mppt) REVERT: I 546 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7867 (mp0) REVERT: I 759 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.8093 (t) REVERT: I 781 ASP cc_start: 0.8260 (t0) cc_final: 0.7834 (t0) REVERT: I 1025 PHE cc_start: 0.6720 (m-10) cc_final: 0.6492 (m-10) REVERT: I 1188 ASP cc_start: 0.9294 (p0) cc_final: 0.9006 (p0) REVERT: I 1233 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8765 (mt) REVERT: J 52 GLU cc_start: 0.7197 (tp30) cc_final: 0.6799 (mm-30) REVERT: J 53 ARG cc_start: 0.8293 (tmt170) cc_final: 0.8056 (tmt170) REVERT: J 69 GLU cc_start: 0.7623 (mp0) cc_final: 0.7322 (mp0) REVERT: J 96 LYS cc_start: 0.8390 (ptpt) cc_final: 0.7843 (pptt) REVERT: J 129 ASP cc_start: 0.7790 (t0) cc_final: 0.7335 (t0) REVERT: J 136 GLU cc_start: 0.8104 (pp20) cc_final: 0.7220 (tp30) REVERT: J 140 TYR cc_start: 0.7732 (m-10) cc_final: 0.6951 (m-10) REVERT: J 144 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7186 (m-10) REVERT: J 180 MET cc_start: 0.8018 (tmm) cc_final: 0.7671 (tmm) REVERT: J 186 GLN cc_start: 0.8048 (tt0) cc_final: 0.7632 (tt0) REVERT: J 237 MET cc_start: 0.9070 (mtt) cc_final: 0.8859 (mtt) REVERT: J 343 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8577 (mm) REVERT: J 375 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7676 (tp30) REVERT: J 747 MET cc_start: 0.7771 (mtp) cc_final: 0.7542 (mtp) REVERT: J 847 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: J 992 LYS cc_start: 0.8165 (mmmt) cc_final: 0.7522 (mtpp) REVERT: J 1040 MET cc_start: 0.5865 (mpp) cc_final: 0.5553 (mpp) REVERT: J 1195 GLN cc_start: 0.7215 (mt0) cc_final: 0.6556 (mp10) REVERT: J 1197 ASN cc_start: 0.7408 (p0) cc_final: 0.6512 (t0) REVERT: J 1342 ASP cc_start: 0.8124 (t0) cc_final: 0.7642 (t0) REVERT: K 11 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7307 (mp0) outliers start: 63 outliers final: 45 residues processed: 354 average time/residue: 0.1865 time to fit residues: 105.4126 Evaluate side-chains 342 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 291 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 759 SER Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 144 TYR Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 602 SER Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 278 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 120 optimal weight: 0.1980 chunk 270 optimal weight: 20.0000 chunk 232 optimal weight: 9.9990 chunk 211 optimal weight: 0.6980 chunk 139 optimal weight: 7.9990 chunk 316 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 462 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.155961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113101 restraints weight = 42045.342| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.59 r_work: 0.3206 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 27422 Z= 0.127 Angle : 0.608 13.952 37475 Z= 0.299 Chirality : 0.047 0.337 4317 Planarity : 0.004 0.044 4556 Dihedral : 14.745 174.256 4561 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.11 % Allowed : 21.27 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.15), residues: 3152 helix: 1.36 (0.16), residues: 1104 sheet: -0.73 (0.28), residues: 339 loop : -0.63 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 202 TYR 0.022 0.001 TYR I1229 PHE 0.037 0.001 PHE I1025 TRP 0.042 0.001 TRP J 115 HIS 0.003 0.001 HIS G 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (27422) covalent geometry : angle 0.60827 / 0.30 (37475) hydrogen bonds : bond 0.03357 / 3.68 ( 1077) hydrogen bonds : angle 4.71697 / 5.18 ( 2939) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 309 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 71 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8637 (mtmt) REVERT: H 185 TYR cc_start: 0.8834 (p90) cc_final: 0.8377 (p90) REVERT: H 197 ASP cc_start: 0.7904 (p0) cc_final: 0.7623 (p0) REVERT: I 47 TYR cc_start: 0.3400 (m-10) cc_final: 0.1183 (m-80) REVERT: I 239 MET cc_start: 0.5346 (tmm) cc_final: 0.4892 (tmm) REVERT: I 443 ASP cc_start: 0.8135 (p0) cc_final: 0.7747 (p0) REVERT: I 496 LYS cc_start: 0.8246 (tttt) cc_final: 0.7433 (mppt) REVERT: I 546 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8037 (mp0) REVERT: I 569 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8985 (tp) REVERT: I 759 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.8286 (t) REVERT: I 1188 ASP cc_start: 0.9359 (p0) cc_final: 0.9064 (p0) REVERT: I 1233 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8906 (mt) REVERT: J 52 GLU cc_start: 0.7285 (tp30) cc_final: 0.6859 (mm-30) REVERT: J 69 GLU cc_start: 0.7710 (mp0) cc_final: 0.7317 (mp0) REVERT: J 96 LYS cc_start: 0.8471 (ptpt) cc_final: 0.7905 (pptt) REVERT: J 129 ASP cc_start: 0.7864 (t0) cc_final: 0.7429 (t0) REVERT: J 136 GLU cc_start: 0.8193 (pp20) cc_final: 0.7392 (tp30) REVERT: J 140 TYR cc_start: 0.7789 (m-10) cc_final: 0.7039 (m-10) REVERT: J 144 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7253 (m-10) REVERT: J 180 MET cc_start: 0.7992 (tmm) cc_final: 0.7618 (tmm) REVERT: J 186 GLN cc_start: 0.8193 (tt0) cc_final: 0.7801 (tt0) REVERT: J 237 MET cc_start: 0.9181 (mtt) cc_final: 0.8977 (mtt) REVERT: J 322 ARG cc_start: 0.7666 (mtm110) cc_final: 0.7168 (mtm180) REVERT: J 343 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8626 (mm) REVERT: J 375 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7836 (tp30) REVERT: J 747 MET cc_start: 0.7974 (mtp) cc_final: 0.7764 (mtp) REVERT: J 847 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7521 (m-30) REVERT: J 992 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7521 (mtpp) REVERT: J 1040 MET cc_start: 0.5915 (mpp) cc_final: 0.5608 (mpp) REVERT: J 1195 GLN cc_start: 0.7260 (mt0) cc_final: 0.6596 (mp10) REVERT: J 1197 ASN cc_start: 0.7433 (p0) cc_final: 0.6497 (t0) REVERT: K 11 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7360 (mp0) outliers start: 57 outliers final: 45 residues processed: 350 average time/residue: 0.1761 time to fit residues: 99.2021 Evaluate side-chains 349 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 759 SER Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 144 TYR Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 355 ILE Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 602 SER Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 94 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 257 optimal weight: 0.0060 chunk 82 optimal weight: 0.0980 chunk 248 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 256 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1061 GLN ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.158865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116770 restraints weight = 41421.995| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.47 r_work: 0.3233 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27422 Z= 0.117 Angle : 0.605 14.125 37475 Z= 0.298 Chirality : 0.046 0.333 4317 Planarity : 0.004 0.048 4556 Dihedral : 14.719 174.094 4561 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.04 % Allowed : 21.53 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.15), residues: 3152 helix: 1.42 (0.16), residues: 1095 sheet: -0.46 (0.29), residues: 320 loop : -0.63 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 535 TYR 0.018 0.001 TYR I1229 PHE 0.043 0.001 PHE G 35 TRP 0.045 0.001 TRP J 115 HIS 0.003 0.001 HIS G 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (27422) covalent geometry : angle 0.60451 / 0.30 (37475) hydrogen bonds : bond 0.03271 / 3.58 ( 1077) hydrogen bonds : angle 4.65880 / 5.11 ( 2939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6535.88 seconds wall clock time: 112 minutes 57.42 seconds (6777.42 seconds total)