Starting phenix.real_space_refine on Sun Aug 9 00:00:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8to6_41437/08_2026/8to6_41437.cif Found real_map, /net/cci-nas-00/data/ceres_data/8to6_41437/08_2026/8to6_41437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8to6_41437/08_2026/8to6_41437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8to6_41437/08_2026/8to6_41437.map" model { file = "/net/cci-nas-00/data/ceres_data/8to6_41437/08_2026/8to6_41437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8to6_41437/08_2026/8to6_41437.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 98 5.49 5 Mg 1 5.21 5 S 130 5.16 5 C 19417 2.51 5 N 5548 2.21 5 O 6210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31406 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1755 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 220} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1699 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10530 Classifications: {'peptide': 1336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1279} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 10373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10373 Classifications: {'peptide': 1335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1278} Chain breaks: 2 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: "K" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "L" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3799 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 455} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "M" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "O" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1150 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "P" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 863 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain breaks: 1 Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'4QM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '4QM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'4QM': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14433 SG CYS J 70 102.739 69.989 74.537 1.00 71.08 S ATOM 14447 SG CYS J 72 101.757 68.367 73.045 1.00 77.12 S ATOM 14555 SG CYS J 85 105.171 69.030 71.683 1.00 75.76 S ATOM 14579 SG CYS J 88 101.383 71.230 71.675 1.00 77.11 S ATOM 20261 SG CYS J 814 131.959 121.172 110.583 1.00 70.47 S ATOM 20826 SG CYS J 888 128.393 120.217 108.879 1.00 36.10 S ATOM 20877 SG CYS J 895 129.835 118.759 112.297 1.00 58.84 S ATOM 20898 SG CYS J 898 129.149 121.535 111.978 1.00 57.65 S Time building chain proxies: 5.03, per 1000 atoms: 0.16 Number of scatterers: 31406 At special positions: 0 Unit cell: (153.608, 196.652, 196.652, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 130 16.00 P 98 15.00 Mg 1 11.99 O 6210 8.00 N 5548 7.00 C 19417 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: 2.33 Conformation dependent library (CDL) restraints added in 941.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " Number of angles added : 12 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6940 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 46 sheets defined 43.6% alpha, 13.9% beta 42 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.629A pdb=" N ASN G 41 " --> pdb=" O HIS G 37 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 4.162A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 212 through 233 removed outlier: 4.175A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.588A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER H 49 " --> pdb=" O ARG H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.646A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 115 Processing helix chain 'H' and resid 212 through 229 Processing helix chain 'I' and resid 28 through 37 removed outlier: 4.027A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.514A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.859A 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 246 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 293 Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 345 through 354 removed outlier: 3.992A pdb=" N GLU I 349 " --> pdb=" O PRO I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 removed outlier: 3.966A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.594A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.623A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 614 removed outlier: 3.771A pdb=" N ASN I 613 " --> pdb=" O GLU I 610 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR I 614 " --> pdb=" O GLU I 611 " (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 670 through 674 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 removed outlier: 4.049A 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 898 through 907 Processing helix chain 'I' and resid 942 through 978 Processing helix chain 'I' and resid 986 through 990 removed outlier: 3.825A pdb=" N LEU I 989 " --> pdb=" O ALA I 986 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASP I 990 " --> pdb=" O GLU I 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 986 through 990' Processing helix chain 'I' and resid 1011 through 1038 Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.562A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1103 removed outlier: 3.568A pdb=" N GLY I1102 " --> pdb=" O ASN I1099 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL I1103 " --> pdb=" O PRO I1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1099 through 1103' Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1149 removed outlier: 3.543A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.614A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.544A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 4.175A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.971A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL I1325 " --> pdb=" O GLU I1321 " (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 114 through 119 removed outlier: 3.605A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) 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 170 removed outlier: 3.523A pdb=" N GLU J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 207 removed outlier: 3.764A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 231 removed outlier: 3.890A pdb=" N GLY J 231 " --> pdb=" O PHE J 227 " (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 263 through 285 removed outlier: 4.093A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP J 284 " --> pdb=" O LYS J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.502A pdb=" N VAL J 292 " --> pdb=" O PRO J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.769A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 4.049A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.840A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL J 592 " --> pdb=" O TYR J 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 588 through 592' Processing helix chain 'J' and resid 597 through 612 removed outlier: 3.719A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER J 602 " --> pdb=" O LYS J 598 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.669A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 735 through 742 removed outlier: 3.578A pdb=" N GLN J 739 " --> pdb=" O ALA J 735 " (cutoff:3.500A) Processing helix chain 'J' and resid 770 through 805 removed outlier: 4.223A pdb=" N ILE J 774 " --> pdb=" O LEU J 770 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA J 784 " --> pdb=" O ARG J 780 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.728A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 removed outlier: 3.551A pdb=" N SER J 887 " --> pdb=" O SER J 884 " (cutoff:3.500A) Processing helix chain 'J' and resid 896 through 900 removed outlier: 3.533A pdb=" N GLY J 900 " --> pdb=" O ALA J 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 896 through 900' Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.729A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 930 Processing helix chain 'J' and resid 1136 through 1146 removed outlier: 3.774A pdb=" N ARG J1140 " --> pdb=" O GLY J1136 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.962A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR J1241 " --> pdb=" O VAL J1237 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.404A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN J1259 " --> pdb=" O VAL J1255 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1313 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.680A pdb=" N PHE J1325 " --> pdb=" O SER J1321 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN J1326 " --> pdb=" O ALA J1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 3.553A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) Processing helix chain 'J' and resid 1348 through 1354 Processing helix chain 'J' and resid 1362 through 1375 Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 32 removed outlier: 3.657A pdb=" N VAL K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.574A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 74 Processing helix chain 'L' and resid 96 through 107 removed outlier: 3.895A pdb=" N THR L 107 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 136 removed outlier: 3.567A pdb=" N GLU L 136 " --> pdb=" O CYS L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 153 removed outlier: 4.162A pdb=" N ILE L 141 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR L 142 " --> pdb=" O PRO L 138 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR L 143 " --> pdb=" O GLU L 139 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 162 removed outlier: 3.813A pdb=" N ILE L 162 " --> pdb=" O LEU L 158 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 233 Processing helix chain 'L' and resid 243 through 258 removed outlier: 4.484A pdb=" N GLU L 247 " --> pdb=" O ALA L 243 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN L 258 " --> pdb=" O GLU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 293 Processing helix chain 'L' and resid 298 through 306 Processing helix chain 'L' and resid 313 through 318 Processing helix chain 'L' and resid 319 through 322 Processing helix chain 'L' and resid 324 through 330 Processing helix chain 'L' and resid 333 through 352 Processing helix chain 'L' and resid 354 through 393 removed outlier: 3.889A pdb=" N GLU L 381 " --> pdb=" O LYS L 377 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA L 382 " --> pdb=" O GLU L 378 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN L 383 " --> pdb=" O MET L 379 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER L 389 " --> pdb=" O ARG L 385 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE L 390 " --> pdb=" O LEU L 386 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 418 Processing helix chain 'L' and resid 426 through 447 removed outlier: 3.717A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 removed outlier: 3.653A pdb=" N GLY L 475 " --> pdb=" O LEU L 471 " (cutoff:3.500A) Processing helix chain 'L' and resid 479 through 487 Processing helix chain 'L' and resid 492 through 500 Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.792A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 551 Processing helix chain 'L' and resid 552 through 563 Processing helix chain 'L' and resid 572 through 581 removed outlier: 3.525A pdb=" N GLN L 579 " --> pdb=" O GLU L 575 " (cutoff:3.500A) Processing helix chain 'L' and resid 584 through 586 No H-bonds generated for 'chain 'L' and resid 584 through 586' Processing helix chain 'L' and resid 588 through 600 Processing helix chain 'L' and resid 605 through 611 Processing helix chain 'M' and resid 251 through 255 removed outlier: 3.589A pdb=" N ARG M 255 " --> pdb=" O PRO M 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 251 through 255' Processing helix chain 'M' and resid 256 through 261 removed outlier: 3.514A pdb=" N GLU M 261 " --> pdb=" O ASP M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 274 Processing helix chain 'M' and resid 277 through 283 Processing helix chain 'M' and resid 285 through 292 removed outlier: 3.957A pdb=" N THR M 292 " --> pdb=" O GLU M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 296 through 310 removed outlier: 3.639A pdb=" N ARG M 310 " --> pdb=" O VAL M 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 17 removed outlier: 8.617A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (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: 4.386A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.516A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 16 through 20 removed outlier: 6.722A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 28 through 31 removed outlier: 5.445A pdb=" N GLU H 29 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU H 201 " --> pdb=" O GLU H 29 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 98 through 105 removed outlier: 7.749A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 109 through 110 Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.815A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.464A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.574A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 159 removed outlier: 5.106A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 284 through 286 removed outlier: 4.835A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU I 226 " --> pdb=" O PHE I 337 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.275A pdb=" N ASP I 303 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU I 309 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.295A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.449A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.568A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC5, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.261A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 846 through 847 removed outlier: 6.361A pdb=" N ASP I 842 " --> pdb=" O VAL I1046 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL I1046 " --> pdb=" O ASP I 842 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 849 through 850 Processing sheet with id=AC9, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.837A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD2, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.962A pdb=" N ALA J 446 " --> pdb=" O PRO J 369 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1268 through 1269 removed outlier: 3.647A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1338 through 1340 Processing sheet with id=AD5, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.472A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 9.762A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AD7, first strand: chain 'J' and resid 252 through 255 removed outlier: 3.888A pdb=" N ARG J 259 " --> pdb=" O LEU J 255 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'J' and resid 703 through 706 Processing sheet with id=AE1, first strand: chain 'J' and resid 809 through 811 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: 3.567A pdb=" N VAL J 825 " --> pdb=" O GLU J 833 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU J 833 " --> 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 848 through 849 removed outlier: 6.701A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.077A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 965 through 967 removed outlier: 3.635A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1079 through 1081 removed outlier: 3.848A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG J1036 " --> pdb=" O LYS J1079 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL J1113 " --> pdb=" O VAL J1035 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.617A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER J1058 " --> pdb=" O GLN J1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1187 through 1190 Processing sheet with id=AF1, first strand: chain 'J' and resid 1279 through 1281 1312 hydrogen bonds defined for protein. 3702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 210 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 8.18 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10213 1.34 - 1.46: 6256 1.46 - 1.58: 15169 1.58 - 1.70: 204 1.70 - 1.83: 235 Bond restraints: 32077 Sorted by residual: bond pdb=" C19 4QM J1504 " pdb=" C3 4QM J1504 " ideal model delta sigma weight residual 1.532 1.828 -0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C19 4QM L 701 " pdb=" C3 4QM L 701 " ideal model delta sigma weight residual 1.532 1.824 -0.292 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C19 4QM I1401 " pdb=" C3 4QM I1401 " ideal model delta sigma weight residual 1.532 1.824 -0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C3 4QM J1504 " pdb=" C4 4QM J1504 " ideal model delta sigma weight residual 1.533 1.727 -0.194 2.00e-02 2.50e+03 9.39e+01 bond pdb=" C3 4QM I1401 " pdb=" C4 4QM I1401 " ideal model delta sigma weight residual 1.533 1.725 -0.192 2.00e-02 2.50e+03 9.18e+01 ... (remaining 32072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 43226 2.55 - 5.10: 494 5.10 - 7.65: 28 7.65 - 10.20: 0 10.20 - 12.75: 1 Bond angle restraints: 43749 Sorted by residual: angle pdb=" C ILE J 707 " pdb=" N ASN J 708 " pdb=" CA ASN J 708 " ideal model delta sigma weight residual 121.70 134.45 -12.75 1.80e+00 3.09e-01 5.01e+01 angle pdb=" N THR I 893 " pdb=" CA THR I 893 " pdb=" CB THR I 893 " ideal model delta sigma weight residual 114.17 107.89 6.28 1.14e+00 7.69e-01 3.03e+01 angle pdb=" N3 DT O 60 " pdb=" C4 DT O 60 " pdb=" O4 DT O 60 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT O 61 " pdb=" C4 DT O 61 " pdb=" O4 DT O 61 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT O 65 " pdb=" C4 DT O 65 " pdb=" O4 DT O 65 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 43744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 19018 35.38 - 70.75: 613 70.75 - 106.13: 24 106.13 - 141.50: 7 141.50 - 176.88: 3 Dihedral angle restraints: 19665 sinusoidal: 8908 harmonic: 10757 Sorted by residual: dihedral pdb=" CA ARG J 425 " pdb=" C ARG J 425 " pdb=" N ALA J 426 " pdb=" CA ALA J 426 " ideal model delta harmonic sigma weight residual -180.00 -155.63 -24.37 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA SER I1332 " pdb=" C SER I1332 " pdb=" N LEU I1333 " pdb=" CA LEU I1333 " ideal model delta harmonic sigma weight residual 180.00 155.68 24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA TRP I 807 " pdb=" C TRP I 807 " pdb=" N ASN I 808 " pdb=" CA ASN I 808 " ideal model delta harmonic sigma weight residual 180.00 155.78 24.22 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 19662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4843 0.116 - 0.232: 168 0.232 - 0.348: 8 0.348 - 0.464: 0 0.464 - 0.580: 4 Chirality restraints: 5023 Sorted by residual: chirality pdb=" P DA O 75 " pdb=" OP1 DA O 75 " pdb=" OP2 DA O 75 " pdb=" O5' DA O 75 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.58 2.00e-01 2.50e+01 8.41e+00 chirality pdb=" P DT O 73 " pdb=" OP1 DT O 73 " pdb=" OP2 DT O 73 " pdb=" O5' DT O 73 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" P DG O 74 " pdb=" OP1 DG O 74 " pdb=" OP2 DG O 74 " pdb=" O5' DG O 74 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.54 2.00e-01 2.50e+01 7.24e+00 ... (remaining 5020 not shown) Planarity restraints: 5344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 423 " 0.460 9.50e-02 1.11e+02 2.06e-01 2.61e+01 pdb=" NE ARG L 423 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG L 423 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG L 423 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG L 423 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG I1223 " -0.041 5.00e-02 4.00e+02 6.26e-02 6.27e+00 pdb=" N PRO I1224 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO I1224 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO I1224 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN L 409 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C ASN L 409 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN L 409 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE L 410 " -0.014 2.00e-02 2.50e+03 ... (remaining 5341 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 225 2.53 - 3.12: 24090 3.12 - 3.71: 45809 3.71 - 4.31: 65088 4.31 - 4.90: 111906 Nonbonded interactions: 247118 Sorted by model distance: nonbonded pdb=" OG1 THR L 234 " pdb=" OE1 GLU L 248 " model vdw 1.933 3.040 nonbonded pdb=" OG1 THR I 91 " pdb=" O ILE I 138 " model vdw 1.965 3.040 nonbonded pdb=" OG SER I1165 " pdb=" OE1 GLU I1168 " model vdw 2.003 3.040 nonbonded pdb=" NH1 ARG I1269 " pdb=" O GLY J 344 " model vdw 2.019 3.120 nonbonded pdb=" O LYS I 593 " pdb=" OG1 THR I 600 " model vdw 2.047 3.040 ... (remaining 247113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 5 through 158 or resid 169 through 234)) selection = (chain 'H' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 190 or (resid 191 and (name N or name CA or name C or name \ O or name CB )) or resid 192 or (resid 193 through 194 and (name N or name CA or \ name C or name O or name CB )) or resid 195 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: 5.440 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: 0.030 Extract box with map and model: 0.730 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 31.430 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.296 32085 Z= 0.384 Angle : 0.775 46.343 43761 Z= 0.428 Chirality : 0.051 0.580 5023 Planarity : 0.005 0.206 5344 Dihedral : 15.577 176.878 12725 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.26 % Favored : 93.66 % Rotamer: Outliers : 4.39 % Allowed : 6.81 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.03 % 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: -0.57 (0.14), residues: 3704 helix: 1.09 (0.14), residues: 1442 sheet: -0.65 (0.24), residues: 452 loop : -1.56 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 44 TYR 0.019 0.002 TYR G 177 PHE 0.011 0.001 PHE I 230 TRP 0.008 0.001 TRP I 807 HIS 0.007 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.38 (32077) covalent geometry : angle 0.67479 / 0.42 (43749) hydrogen bonds : bond 0.15698 / 10.82 ( 1415) hydrogen bonds : angle 6.18713 / 4.27 ( 3912) metal coordination : bond 0.06183 / 3.71 ( 8) metal coordination : angle 23.07971 / 13.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 552 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 ARG cc_start: 0.7623 (ptp90) cc_final: 0.7406 (ptp90) REVERT: G 67 GLU cc_start: 0.8261 (pt0) cc_final: 0.8003 (pt0) REVERT: G 95 LYS cc_start: 0.8487 (mtmm) cc_final: 0.8156 (mtpt) REVERT: G 125 LYS cc_start: 0.8765 (tttt) cc_final: 0.8530 (tttm) REVERT: G 197 ASP cc_start: 0.7630 (p0) cc_final: 0.7060 (p0) REVERT: G 204 GLU cc_start: 0.8237 (tt0) cc_final: 0.7898 (mt-10) REVERT: H 58 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6902 (mt-10) REVERT: H 214 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6436 (pm20) REVERT: I 70 TYR cc_start: 0.8398 (t80) cc_final: 0.8154 (t80) REVERT: I 142 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8117 (mt-10) REVERT: I 197 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6659 (mtm-85) REVERT: I 284 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.6811 (tt) REVERT: I 642 SER cc_start: 0.9010 (p) cc_final: 0.8789 (t) REVERT: I 643 SER cc_start: 0.8358 (p) cc_final: 0.8114 (m) REVERT: I 672 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8027 (pm20) REVERT: I 696 ASP cc_start: 0.8623 (t0) cc_final: 0.8398 (t70) REVERT: I 768 MET cc_start: 0.8891 (ptm) cc_final: 0.8685 (ptp) REVERT: I 791 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9038 (mp) REVERT: I 866 ASP cc_start: 0.8161 (p0) cc_final: 0.7782 (p0) REVERT: I 954 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7581 (mttm) REVERT: I 1254 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8484 (t) REVERT: J 66 LYS cc_start: 0.7469 (mtmm) cc_final: 0.7263 (pttm) REVERT: J 227 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7491 (t80) REVERT: J 280 LYS cc_start: 0.8011 (mtmt) cc_final: 0.7766 (mtpt) REVERT: J 290 ILE cc_start: 0.8211 (mp) cc_final: 0.7978 (tt) REVERT: J 416 ILE cc_start: 0.8816 (mm) cc_final: 0.8487 (pt) REVERT: J 738 ARG cc_start: 0.7968 (ttm170) cc_final: 0.7760 (mtm110) REVERT: J 781 LYS cc_start: 0.8206 (tptm) cc_final: 0.7933 (ttmm) REVERT: J 1040 MET cc_start: 0.0191 (tpt) cc_final: -0.2424 (mtt) REVERT: J 1311 LYS cc_start: 0.7572 (tppp) cc_final: 0.7354 (ttmm) REVERT: J 1367 GLN cc_start: 0.7455 (mt0) cc_final: 0.7191 (mm110) outliers start: 140 outliers final: 57 residues processed: 664 average time/residue: 0.7276 time to fit residues: 563.8221 Evaluate side-chains 454 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 390 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 197 ARG Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 483 ASP Chi-restraints excluded: chain I residue 549 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 635 SER Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain L residue 402 LEU Chi-restraints excluded: chain L residue 483 LEU Chi-restraints excluded: chain L residue 517 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 66 HIS G 186 ASN H 147 GLN H 186 ASN H 227 GLN I 799 ASN I 811 ASN J 94 GLN J 335 GLN J 651 HIS J 777 HIS J1326 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.205034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.122547 restraints weight = 34508.969| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.17 r_work: 0.3163 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 32085 Z= 0.206 Angle : 0.687 20.056 43761 Z= 0.355 Chirality : 0.047 0.373 5023 Planarity : 0.005 0.063 5344 Dihedral : 16.417 178.046 5477 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.02 % Favored : 94.92 % Rotamer: Outliers : 4.93 % Allowed : 13.34 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.03 % 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: -0.26 (0.14), residues: 3704 helix: 1.37 (0.14), residues: 1463 sheet: -0.66 (0.24), residues: 450 loop : -1.38 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 274 TYR 0.021 0.002 TYR J 144 PHE 0.028 0.002 PHE L 580 TRP 0.011 0.001 TRP I 997 HIS 0.008 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (32077) covalent geometry : angle 0.67297 / 0.35 (43749) hydrogen bonds : bond 0.05672 / 3.92 ( 1415) hydrogen bonds : angle 4.82967 / 3.38 ( 3912) metal coordination : bond 0.01202 / 0.63 ( 8) metal coordination : angle 8.33628 / 4.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 402 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 44 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.7861 (ttt90) REVERT: G 67 GLU cc_start: 0.8194 (pt0) cc_final: 0.7902 (pt0) REVERT: G 95 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8336 (mttp) REVERT: G 125 LYS cc_start: 0.8709 (tttt) cc_final: 0.8462 (tttm) REVERT: G 197 ASP cc_start: 0.7902 (p0) cc_final: 0.7346 (p0) REVERT: H 110 VAL cc_start: 0.8285 (t) cc_final: 0.8048 (p) REVERT: H 214 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6333 (pm20) REVERT: I 37 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7614 (mtpt) REVERT: I 70 TYR cc_start: 0.8375 (t80) cc_final: 0.8138 (t80) REVERT: I 142 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8242 (mt-10) REVERT: I 197 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6675 (mtm180) REVERT: I 203 LYS cc_start: 0.8671 (mtpm) cc_final: 0.8421 (mtpp) REVERT: I 334 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7668 (mt-10) REVERT: I 510 GLN cc_start: 0.8609 (tt0) cc_final: 0.8394 (tm-30) REVERT: I 603 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8566 (mp) REVERT: I 642 SER cc_start: 0.8957 (p) cc_final: 0.8685 (t) REVERT: I 643 SER cc_start: 0.8226 (p) cc_final: 0.7984 (m) REVERT: I 672 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7996 (pm20) REVERT: I 696 ASP cc_start: 0.8370 (t0) cc_final: 0.8129 (t70) REVERT: I 768 MET cc_start: 0.8944 (ptm) cc_final: 0.8732 (ptp) REVERT: I 791 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8906 (mp) REVERT: I 799 ASN cc_start: 0.8935 (OUTLIER) cc_final: 0.8612 (m110) REVERT: I 859 GLU cc_start: 0.6887 (tp30) cc_final: 0.6583 (tp30) REVERT: I 876 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7986 (mp0) REVERT: I 954 LYS cc_start: 0.7877 (mtpt) cc_final: 0.7519 (mttm) REVERT: I 1170 MET cc_start: 0.8773 (mmp) cc_final: 0.8524 (mmt) REVERT: I 1254 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8468 (t) REVERT: I 1290 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8766 (mmt) REVERT: J 66 LYS cc_start: 0.7491 (mtmm) cc_final: 0.7061 (pttm) REVERT: J 69 GLU cc_start: 0.8466 (pt0) cc_final: 0.8135 (pt0) REVERT: J 97 VAL cc_start: 0.8966 (p) cc_final: 0.8663 (m) REVERT: J 158 GLN cc_start: 0.7952 (tt0) cc_final: 0.7337 (tt0) REVERT: J 280 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7564 (mtpt) REVERT: J 399 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7879 (mptt) REVERT: J 649 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7614 (ptmt) REVERT: J 740 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8580 (mt) REVERT: J 781 LYS cc_start: 0.8340 (tptm) cc_final: 0.7847 (mtmm) REVERT: J 822 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.5719 (mpt) REVERT: J 925 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: J 1040 MET cc_start: 0.0584 (tpt) cc_final: -0.2013 (mtt) REVERT: J 1311 LYS cc_start: 0.7599 (tppp) cc_final: 0.7372 (ttmm) REVERT: J 1341 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8082 (ttt180) REVERT: J 1367 GLN cc_start: 0.7296 (mt0) cc_final: 0.6918 (mm110) REVERT: K 69 ARG cc_start: 0.7364 (ttp80) cc_final: 0.6992 (ttp80) REVERT: L 116 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8150 (mp0) REVERT: L 165 PHE cc_start: 0.6766 (m-10) cc_final: 0.4674 (m-10) REVERT: L 378 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: L 421 TYR cc_start: 0.8573 (p90) cc_final: 0.8350 (p90) outliers start: 157 outliers final: 73 residues processed: 520 average time/residue: 0.6256 time to fit residues: 386.7001 Evaluate side-chains 446 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 357 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 197 ARG Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1341 ARG Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain L residue 378 GLU Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 402 LEU Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 483 LEU Chi-restraints excluded: chain M residue 270 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 141 optimal weight: 4.9990 chunk 315 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 374 optimal weight: 50.0000 chunk 5 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 303 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 354 optimal weight: 0.9980 chunk 198 optimal weight: 5.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 186 ASN H 103 ASN I 526 HIS I 618 GLN I 760 ASN I 811 ASN I1244 HIS J 335 GLN J 651 HIS J 777 HIS J 875 ASN J1326 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.205547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126591 restraints weight = 34500.276| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.74 r_work: 0.3169 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32085 Z= 0.179 Angle : 0.618 15.441 43761 Z= 0.324 Chirality : 0.045 0.352 5023 Planarity : 0.005 0.068 5344 Dihedral : 15.945 177.897 5448 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.65 % Allowed : 14.50 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.03 % 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: -0.09 (0.14), residues: 3704 helix: 1.50 (0.14), residues: 1478 sheet: -0.57 (0.24), residues: 446 loop : -1.31 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 388 TYR 0.024 0.001 TYR J 144 PHE 0.017 0.002 PHE I 906 TRP 0.012 0.001 TRP I 997 HIS 0.006 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (32077) covalent geometry : angle 0.60730 / 0.32 (43749) hydrogen bonds : bond 0.05047 / 3.51 ( 1415) hydrogen bonds : angle 4.54627 / 3.20 ( 3912) metal coordination : bond 0.00788 / 0.42 ( 8) metal coordination : angle 7.01619 / 4.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 380 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 67 GLU cc_start: 0.8159 (pt0) cc_final: 0.7855 (pt0) REVERT: G 95 LYS cc_start: 0.8589 (mtmm) cc_final: 0.8324 (mttp) REVERT: G 125 LYS cc_start: 0.8672 (tttt) cc_final: 0.8439 (tttm) REVERT: G 186 ASN cc_start: 0.8437 (m-40) cc_final: 0.7854 (m110) REVERT: G 187 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8676 (t) REVERT: G 197 ASP cc_start: 0.7913 (p0) cc_final: 0.7418 (p0) REVERT: H 174 ASP cc_start: 0.8683 (m-30) cc_final: 0.8479 (m-30) REVERT: I 37 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7607 (mtpt) REVERT: I 197 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6578 (mtm-85) REVERT: I 203 LYS cc_start: 0.8725 (mtpm) cc_final: 0.8395 (mtpm) REVERT: I 334 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7729 (mt-10) REVERT: I 510 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8387 (tm-30) REVERT: I 546 GLU cc_start: 0.7191 (pm20) cc_final: 0.6766 (mp0) REVERT: I 603 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8552 (mp) REVERT: I 642 SER cc_start: 0.8907 (p) cc_final: 0.8627 (t) REVERT: I 643 SER cc_start: 0.8293 (p) cc_final: 0.8024 (m) REVERT: I 672 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.7938 (pm20) REVERT: I 768 MET cc_start: 0.8951 (ptm) cc_final: 0.8745 (ptp) REVERT: I 791 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8913 (mp) REVERT: I 799 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8726 (m110) REVERT: I 859 GLU cc_start: 0.6950 (tp30) cc_final: 0.6630 (tp30) REVERT: I 954 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7525 (mttm) REVERT: I 1090 ASN cc_start: 0.8272 (t0) cc_final: 0.7840 (m110) REVERT: I 1203 ASP cc_start: 0.7363 (m-30) cc_final: 0.7154 (m-30) REVERT: I 1254 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8448 (t) REVERT: I 1290 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8747 (mmt) REVERT: J 66 LYS cc_start: 0.7468 (mtmm) cc_final: 0.7011 (pttm) REVERT: J 69 GLU cc_start: 0.8459 (pt0) cc_final: 0.8162 (pt0) REVERT: J 97 VAL cc_start: 0.8946 (p) cc_final: 0.8643 (m) REVERT: J 154 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5809 (pp) REVERT: J 158 GLN cc_start: 0.7924 (tt0) cc_final: 0.7322 (tt0) REVERT: J 227 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7279 (t80) REVERT: J 280 LYS cc_start: 0.7869 (mtmt) cc_final: 0.7465 (mtpt) REVERT: J 399 LYS cc_start: 0.8114 (mmtp) cc_final: 0.7823 (mptt) REVERT: J 525 MET cc_start: 0.9038 (mtm) cc_final: 0.8792 (mtm) REVERT: J 545 HIS cc_start: 0.8958 (OUTLIER) cc_final: 0.8694 (m90) REVERT: J 781 LYS cc_start: 0.8277 (tptm) cc_final: 0.7796 (mtmm) REVERT: J 822 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.5567 (mpt) REVERT: J 1040 MET cc_start: 0.0687 (tpt) cc_final: -0.1892 (mtt) REVERT: J 1311 LYS cc_start: 0.7519 (tppp) cc_final: 0.7318 (ttmm) REVERT: J 1341 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8070 (ttt180) REVERT: J 1367 GLN cc_start: 0.7322 (mt0) cc_final: 0.6914 (mm110) REVERT: K 38 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8248 (mt) REVERT: L 116 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8141 (mp0) REVERT: L 125 ASP cc_start: 0.9058 (t0) cc_final: 0.8842 (t0) REVERT: L 129 GLN cc_start: 0.8974 (mt0) cc_final: 0.8408 (mt0) REVERT: L 378 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: L 458 GLU cc_start: 0.8279 (tp30) cc_final: 0.7936 (tp30) outliers start: 148 outliers final: 73 residues processed: 492 average time/residue: 0.6213 time to fit residues: 364.0153 Evaluate side-chains 428 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 338 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 197 ARG Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 799 ASN Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1322 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1341 ARG Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain L residue 378 GLU Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 402 LEU Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 483 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 72 optimal weight: 30.0000 chunk 58 optimal weight: 0.7980 chunk 209 optimal weight: 3.9990 chunk 226 optimal weight: 0.0980 chunk 78 optimal weight: 9.9990 chunk 143 optimal weight: 50.0000 chunk 310 optimal weight: 3.9990 chunk 349 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 212 optimal weight: 0.3980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 103 ASN H 147 GLN I 811 ASN I1244 HIS J 335 GLN J 651 HIS J 777 HIS J 865 HIS J1010 GLN J1326 GLN L 579 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.206801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122222 restraints weight = 34457.666| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.36 r_work: 0.3160 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32085 Z= 0.136 Angle : 0.576 12.280 43761 Z= 0.303 Chirality : 0.043 0.342 5023 Planarity : 0.004 0.063 5344 Dihedral : 15.842 177.771 5438 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.49 % Allowed : 15.60 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.03 % 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: 0.09 (0.14), residues: 3704 helix: 1.73 (0.14), residues: 1472 sheet: -0.58 (0.24), residues: 456 loop : -1.23 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 388 TYR 0.020 0.001 TYR J 144 PHE 0.022 0.001 PHE L 580 TRP 0.009 0.001 TRP I 997 HIS 0.007 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (32077) covalent geometry : angle 0.56721 / 0.30 (43749) hydrogen bonds : bond 0.04454 / 3.10 ( 1415) hydrogen bonds : angle 4.37686 / 3.08 ( 3912) metal coordination : bond 0.00562 / 0.29 ( 8) metal coordination : angle 5.99802 / 3.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 362 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 67 GLU cc_start: 0.8212 (pt0) cc_final: 0.7910 (pt0) REVERT: G 80 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: G 95 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8307 (mttp) REVERT: G 125 LYS cc_start: 0.8690 (tttt) cc_final: 0.8426 (tttm) REVERT: G 186 ASN cc_start: 0.8500 (m-40) cc_final: 0.7937 (m110) REVERT: G 197 ASP cc_start: 0.7931 (p0) cc_final: 0.7472 (p0) REVERT: I 124 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8484 (ptm) REVERT: I 151 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8375 (ttm170) REVERT: I 197 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6576 (mtm-85) REVERT: I 203 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8425 (mtpm) REVERT: I 334 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7736 (mt-10) REVERT: I 546 GLU cc_start: 0.7063 (pm20) cc_final: 0.6694 (mp0) REVERT: I 603 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8518 (mp) REVERT: I 642 SER cc_start: 0.8889 (p) cc_final: 0.8568 (t) REVERT: I 643 SER cc_start: 0.8265 (p) cc_final: 0.7976 (m) REVERT: I 672 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.7853 (pm20) REVERT: I 699 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8445 (mp) REVERT: I 768 MET cc_start: 0.8985 (ptm) cc_final: 0.8783 (ptp) REVERT: I 791 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8881 (mp) REVERT: I 859 GLU cc_start: 0.6998 (tp30) cc_final: 0.6619 (tp30) REVERT: I 876 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7883 (mp0) REVERT: I 954 LYS cc_start: 0.7884 (mtpt) cc_final: 0.7521 (mttm) REVERT: I 1082 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8358 (mt) REVERT: I 1090 ASN cc_start: 0.8275 (t0) cc_final: 0.7852 (m110) REVERT: I 1203 ASP cc_start: 0.7406 (m-30) cc_final: 0.7188 (m-30) REVERT: I 1233 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8819 (mt) REVERT: I 1290 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8759 (mmt) REVERT: I 1319 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7816 (ttp) REVERT: J 66 LYS cc_start: 0.7459 (mtmm) cc_final: 0.6970 (pttm) REVERT: J 69 GLU cc_start: 0.8492 (pt0) cc_final: 0.8170 (pt0) REVERT: J 97 VAL cc_start: 0.8950 (p) cc_final: 0.8646 (m) REVERT: J 154 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5708 (pp) REVERT: J 158 GLN cc_start: 0.7910 (tt0) cc_final: 0.7411 (tt0) REVERT: J 192 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7349 (ttm) REVERT: J 280 LYS cc_start: 0.7789 (mtmt) cc_final: 0.7372 (mtpt) REVERT: J 525 MET cc_start: 0.9055 (mtm) cc_final: 0.8792 (mtm) REVERT: J 738 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8241 (mtt90) REVERT: J 781 LYS cc_start: 0.8345 (tptm) cc_final: 0.7783 (mtmm) REVERT: J 822 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.5578 (mpt) REVERT: J 1040 MET cc_start: 0.0765 (tpt) cc_final: -0.1825 (mtt) REVERT: J 1311 LYS cc_start: 0.7517 (tppp) cc_final: 0.7298 (ttmm) REVERT: J 1341 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7926 (ttt180) REVERT: J 1343 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6920 (mm-30) REVERT: J 1367 GLN cc_start: 0.7319 (mt0) cc_final: 0.6850 (mm110) REVERT: K 69 ARG cc_start: 0.7092 (tmm-80) cc_final: 0.6867 (tmm-80) REVERT: L 116 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8129 (mp0) REVERT: L 125 ASP cc_start: 0.9132 (t0) cc_final: 0.8843 (t0) REVERT: L 458 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7979 (tp30) outliers start: 143 outliers final: 73 residues processed: 468 average time/residue: 0.6614 time to fit residues: 371.0142 Evaluate side-chains 435 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 342 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 197 ARG Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1174 GLU Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain I residue 1322 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 738 ARG Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1341 ARG Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 402 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 458 GLU Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 483 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 101 optimal weight: 0.8980 chunk 368 optimal weight: 50.0000 chunk 325 optimal weight: 50.0000 chunk 168 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 277 optimal weight: 30.0000 chunk 82 optimal weight: 8.9990 chunk 226 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 283 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 147 GLN I 799 ASN I 811 ASN I 834 GLN I1244 HIS J 335 GLN J 651 HIS J 777 HIS J 865 HIS J 867 GLN J1326 GLN L 131 GLN L 579 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.206476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126777 restraints weight = 34452.094| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.97 r_work: 0.3210 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32085 Z= 0.145 Angle : 0.574 13.261 43761 Z= 0.301 Chirality : 0.043 0.348 5023 Planarity : 0.004 0.056 5344 Dihedral : 15.768 177.755 5431 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.65 % Allowed : 15.47 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.03 % 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: 0.16 (0.14), residues: 3704 helix: 1.72 (0.14), residues: 1488 sheet: -0.52 (0.24), residues: 458 loop : -1.17 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 388 TYR 0.017 0.001 TYR G 177 PHE 0.024 0.001 PHE L 266 TRP 0.008 0.001 TRP I 997 HIS 0.007 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (32077) covalent geometry : angle 0.56708 / 0.30 (43749) hydrogen bonds : bond 0.04398 / 3.06 ( 1415) hydrogen bonds : angle 4.30904 / 3.04 ( 3912) metal coordination : bond 0.00536 / 0.28 ( 8) metal coordination : angle 5.54091 / 3.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 358 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 67 GLU cc_start: 0.8139 (pt0) cc_final: 0.7832 (pt0) REVERT: G 80 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: G 125 LYS cc_start: 0.8707 (tttt) cc_final: 0.8432 (tttm) REVERT: G 129 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8263 (t) REVERT: G 186 ASN cc_start: 0.8520 (m-40) cc_final: 0.7964 (m110) REVERT: G 197 ASP cc_start: 0.7931 (p0) cc_final: 0.7506 (p0) REVERT: I 37 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7619 (mtpt) REVERT: I 151 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8311 (ttm170) REVERT: I 197 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6659 (mtm180) REVERT: I 203 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8364 (mtpm) REVERT: I 284 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.6862 (tm) REVERT: I 334 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7756 (mt-10) REVERT: I 510 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: I 546 GLU cc_start: 0.7049 (pm20) cc_final: 0.6715 (mp0) REVERT: I 603 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8504 (mp) REVERT: I 642 SER cc_start: 0.8892 (p) cc_final: 0.8561 (t) REVERT: I 643 SER cc_start: 0.8295 (p) cc_final: 0.7987 (m) REVERT: I 672 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: I 699 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8445 (mp) REVERT: I 768 MET cc_start: 0.8942 (ptm) cc_final: 0.8696 (ptp) REVERT: I 791 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8864 (mp) REVERT: I 814 ASP cc_start: 0.8142 (m-30) cc_final: 0.7913 (m-30) REVERT: I 859 GLU cc_start: 0.6948 (tp30) cc_final: 0.6557 (tp30) REVERT: I 876 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7838 (mp0) REVERT: I 954 LYS cc_start: 0.7853 (mtpt) cc_final: 0.7504 (mttm) REVERT: I 1082 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8374 (mt) REVERT: I 1090 ASN cc_start: 0.8241 (t0) cc_final: 0.7861 (m110) REVERT: I 1188 ASP cc_start: 0.8967 (p0) cc_final: 0.8553 (p0) REVERT: I 1203 ASP cc_start: 0.7265 (m-30) cc_final: 0.7046 (m-30) REVERT: I 1233 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8777 (mt) REVERT: I 1290 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8731 (mmt) REVERT: I 1319 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7786 (ttp) REVERT: J 66 LYS cc_start: 0.7404 (mtmm) cc_final: 0.6929 (pttm) REVERT: J 69 GLU cc_start: 0.8411 (pt0) cc_final: 0.8105 (pt0) REVERT: J 97 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8622 (m) REVERT: J 154 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5706 (pp) REVERT: J 158 GLN cc_start: 0.7905 (tt0) cc_final: 0.7422 (mt0) REVERT: J 227 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7176 (t80) REVERT: J 525 MET cc_start: 0.9058 (mtm) cc_final: 0.8805 (mtm) REVERT: J 738 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8176 (mtt90) REVERT: J 781 LYS cc_start: 0.8338 (tptm) cc_final: 0.7970 (ttmm) REVERT: J 822 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.5566 (mpt) REVERT: J 1040 MET cc_start: 0.0451 (tpt) cc_final: -0.2019 (mtt) REVERT: J 1311 LYS cc_start: 0.7493 (tppp) cc_final: 0.7285 (ttmm) REVERT: J 1341 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7901 (ttt180) REVERT: J 1343 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6821 (mm-30) REVERT: J 1367 GLN cc_start: 0.7315 (mt0) cc_final: 0.6909 (mm110) REVERT: K 69 ARG cc_start: 0.7184 (tmm-80) cc_final: 0.6904 (tmm-80) REVERT: L 125 ASP cc_start: 0.9095 (t0) cc_final: 0.8789 (t0) REVERT: L 259 PHE cc_start: 0.7527 (m-80) cc_final: 0.7247 (m-80) REVERT: L 395 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7943 (m) REVERT: L 458 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7899 (tp30) REVERT: L 574 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8392 (mm-30) outliers start: 148 outliers final: 81 residues processed: 467 average time/residue: 0.6358 time to fit residues: 356.4544 Evaluate side-chains 453 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 347 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 197 ARG Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1028 LYS Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1089 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain I residue 1322 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 738 ARG Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1341 ARG Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain L residue 131 GLN Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 402 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 458 GLU Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 483 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 317 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 250 optimal weight: 0.6980 chunk 345 optimal weight: 0.2980 chunk 255 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 376 optimal weight: 50.0000 chunk 73 optimal weight: 5.9990 chunk 321 optimal weight: 20.0000 chunk 199 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 147 GLN I 387 ASN I 811 ASN I1244 HIS J 335 GLN J 651 HIS J 777 HIS J 865 HIS J 867 GLN J1326 GLN L 579 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.206030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.117875 restraints weight = 34249.081| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.97 r_work: 0.3142 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32085 Z= 0.164 Angle : 0.589 14.609 43761 Z= 0.307 Chirality : 0.044 0.356 5023 Planarity : 0.004 0.056 5344 Dihedral : 15.752 179.913 5430 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.77 % Allowed : 15.66 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.03 % 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: 0.19 (0.14), residues: 3704 helix: 1.73 (0.14), residues: 1487 sheet: -0.46 (0.24), residues: 453 loop : -1.15 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J1284 TYR 0.023 0.001 TYR J 144 PHE 0.013 0.001 PHE L 165 TRP 0.008 0.001 TRP I 997 HIS 0.007 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (32077) covalent geometry : angle 0.58278 / 0.31 (43749) hydrogen bonds : bond 0.04504 / 3.13 ( 1415) hydrogen bonds : angle 4.29838 / 3.04 ( 3912) metal coordination : bond 0.00568 / 0.31 ( 8) metal coordination : angle 5.20676 / 3.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 354 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 67 GLU cc_start: 0.8250 (pt0) cc_final: 0.7959 (pt0) REVERT: G 80 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7865 (mt-10) REVERT: G 125 LYS cc_start: 0.8709 (tttt) cc_final: 0.8420 (tttm) REVERT: G 129 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8268 (t) REVERT: G 186 ASN cc_start: 0.8568 (m-40) cc_final: 0.8013 (m110) REVERT: G 197 ASP cc_start: 0.7999 (p0) cc_final: 0.7588 (p0) REVERT: I 37 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7686 (mtpt) REVERT: I 151 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8406 (ttm170) REVERT: I 197 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6710 (mtm180) REVERT: I 203 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8404 (mtpm) REVERT: I 284 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.6903 (tp) REVERT: I 334 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7788 (mt-10) REVERT: I 510 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: I 603 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8542 (mp) REVERT: I 642 SER cc_start: 0.8920 (p) cc_final: 0.8580 (t) REVERT: I 643 SER cc_start: 0.8333 (p) cc_final: 0.8024 (m) REVERT: I 672 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.7869 (pm20) REVERT: I 768 MET cc_start: 0.8996 (ptm) cc_final: 0.8755 (ptp) REVERT: I 791 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8868 (mp) REVERT: I 859 GLU cc_start: 0.7003 (tp30) cc_final: 0.6584 (tp30) REVERT: I 876 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7890 (mp0) REVERT: I 954 LYS cc_start: 0.7912 (mtpt) cc_final: 0.7552 (mttm) REVERT: I 1028 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7505 (tptm) REVERT: I 1082 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8355 (mt) REVERT: I 1090 ASN cc_start: 0.8331 (t0) cc_final: 0.7895 (m110) REVERT: I 1188 ASP cc_start: 0.8963 (p0) cc_final: 0.8549 (p0) REVERT: I 1233 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8841 (mt) REVERT: I 1290 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8764 (mmt) REVERT: I 1319 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7853 (ttp) REVERT: J 42 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: J 66 LYS cc_start: 0.7465 (mtmm) cc_final: 0.6936 (pttm) REVERT: J 69 GLU cc_start: 0.8501 (pt0) cc_final: 0.8185 (pt0) REVERT: J 97 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8619 (m) REVERT: J 154 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5669 (pp) REVERT: J 158 GLN cc_start: 0.7925 (tt0) cc_final: 0.7439 (tt0) REVERT: J 227 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7134 (t80) REVERT: J 525 MET cc_start: 0.9083 (mtm) cc_final: 0.8818 (mtm) REVERT: J 603 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7961 (ttmm) REVERT: J 781 LYS cc_start: 0.8383 (tptm) cc_final: 0.7996 (ttmm) REVERT: J 822 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.5535 (mpt) REVERT: J 1040 MET cc_start: 0.0558 (tpt) cc_final: -0.1925 (mtt) REVERT: J 1311 LYS cc_start: 0.7506 (tppp) cc_final: 0.7293 (ttmm) REVERT: J 1341 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7920 (ttt180) REVERT: J 1343 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6899 (mm-30) REVERT: J 1367 GLN cc_start: 0.7281 (mt0) cc_final: 0.6820 (mm110) REVERT: K 69 ARG cc_start: 0.7137 (tmm-80) cc_final: 0.6830 (tmm-80) REVERT: L 125 ASP cc_start: 0.9158 (t0) cc_final: 0.8795 (t0) REVERT: L 129 GLN cc_start: 0.9055 (mt0) cc_final: 0.8759 (mp10) REVERT: L 259 PHE cc_start: 0.7687 (m-80) cc_final: 0.7482 (m-80) REVERT: L 395 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8000 (m) REVERT: L 458 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8032 (tp30) REVERT: L 470 MET cc_start: 0.8411 (mtm) cc_final: 0.8132 (mtp) outliers start: 152 outliers final: 90 residues processed: 468 average time/residue: 0.6095 time to fit residues: 342.2256 Evaluate side-chains 463 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 347 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 197 ARG Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 791 LEU Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1028 LYS Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1089 GLU Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 603 LYS Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1341 ARG Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 402 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 458 GLU Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 483 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 280 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 306 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 350 optimal weight: 3.9990 chunk 302 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 147 GLN I 387 ASN I 811 ASN I1244 HIS J 651 HIS J 777 HIS J 865 HIS J 867 GLN J1326 GLN L 131 GLN L 579 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.206191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.123007 restraints weight = 34357.689| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.27 r_work: 0.3174 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 32085 Z= 0.156 Angle : 0.585 15.847 43761 Z= 0.305 Chirality : 0.043 0.355 5023 Planarity : 0.004 0.055 5344 Dihedral : 15.721 178.057 5430 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.49 % Allowed : 16.60 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.03 % 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: 0.23 (0.14), residues: 3704 helix: 1.77 (0.14), residues: 1480 sheet: -0.41 (0.24), residues: 451 loop : -1.13 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 388 TYR 0.025 0.001 TYR J 144 PHE 0.026 0.001 PHE L 266 TRP 0.007 0.001 TRP I 997 HIS 0.007 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (32077) covalent geometry : angle 0.57959 / 0.30 (43749) hydrogen bonds : bond 0.04421 / 3.07 ( 1415) hydrogen bonds : angle 4.27429 / 3.03 ( 3912) metal coordination : bond 0.00533 / 0.29 ( 8) metal coordination : angle 4.98202 / 2.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 364 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 67 GLU cc_start: 0.8206 (pt0) cc_final: 0.7908 (pt0) REVERT: G 80 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: G 125 LYS cc_start: 0.8663 (tttt) cc_final: 0.8374 (tttm) REVERT: G 129 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8250 (t) REVERT: G 186 ASN cc_start: 0.8539 (m-40) cc_final: 0.7965 (m110) REVERT: G 197 ASP cc_start: 0.8013 (p0) cc_final: 0.7617 (p0) REVERT: I 37 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7659 (mtpt) REVERT: I 88 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7859 (ttm170) REVERT: I 151 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8359 (ttm170) REVERT: I 197 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6602 (mtm-85) REVERT: I 203 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8364 (mtpm) REVERT: I 284 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.6901 (tm) REVERT: I 334 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7800 (mt-10) REVERT: I 414 ILE cc_start: 0.8350 (tt) cc_final: 0.8120 (tt) REVERT: I 510 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: I 642 SER cc_start: 0.8901 (p) cc_final: 0.8592 (t) REVERT: I 643 SER cc_start: 0.8305 (p) cc_final: 0.7992 (m) REVERT: I 672 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.7866 (pm20) REVERT: I 768 MET cc_start: 0.8971 (ptm) cc_final: 0.8734 (ptp) REVERT: I 859 GLU cc_start: 0.6961 (tp30) cc_final: 0.6589 (tp30) REVERT: I 876 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7861 (mp0) REVERT: I 916 SER cc_start: 0.8403 (t) cc_final: 0.7776 (p) REVERT: I 954 LYS cc_start: 0.7863 (mtpt) cc_final: 0.7507 (mttm) REVERT: I 1028 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7500 (tptm) REVERT: I 1082 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8361 (mt) REVERT: I 1090 ASN cc_start: 0.8289 (t0) cc_final: 0.7894 (m-40) REVERT: I 1188 ASP cc_start: 0.8921 (p0) cc_final: 0.8531 (p0) REVERT: I 1233 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8825 (mt) REVERT: I 1290 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8753 (mmt) REVERT: I 1319 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7816 (ttp) REVERT: J 42 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7755 (mt-10) REVERT: J 66 LYS cc_start: 0.7409 (mtmm) cc_final: 0.6847 (pttm) REVERT: J 69 GLU cc_start: 0.8461 (pt0) cc_final: 0.8095 (pt0) REVERT: J 97 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8618 (m) REVERT: J 154 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5564 (pp) REVERT: J 158 GLN cc_start: 0.7915 (tt0) cc_final: 0.7438 (tt0) REVERT: J 227 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.7120 (t80) REVERT: J 525 MET cc_start: 0.9087 (mtm) cc_final: 0.8831 (mtm) REVERT: J 603 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7929 (ttmm) REVERT: J 744 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8511 (tmt-80) REVERT: J 781 LYS cc_start: 0.8336 (tptm) cc_final: 0.7935 (ttmm) REVERT: J 822 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.5464 (mpt) REVERT: J 1040 MET cc_start: 0.0383 (tpt) cc_final: -0.2041 (mtt) REVERT: J 1311 LYS cc_start: 0.7447 (tppp) cc_final: 0.7223 (ttmm) REVERT: J 1341 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7906 (ttt180) REVERT: J 1343 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6893 (mm-30) REVERT: J 1367 GLN cc_start: 0.7238 (mt0) cc_final: 0.6780 (mm110) REVERT: K 69 ARG cc_start: 0.7150 (tmm-80) cc_final: 0.6946 (tmm-80) REVERT: L 125 ASP cc_start: 0.9127 (t0) cc_final: 0.8837 (t0) REVERT: L 395 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.7993 (m) REVERT: L 458 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7928 (tp30) outliers start: 143 outliers final: 91 residues processed: 472 average time/residue: 0.6507 time to fit residues: 367.9457 Evaluate side-chains 469 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 352 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 197 ARG Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1028 LYS Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1089 GLU Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 568 SER Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 603 LYS Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 744 ARG Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 867 GLN Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1341 ARG Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 402 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 458 GLU Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 483 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 188 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 346 optimal weight: 9.9990 chunk 170 optimal weight: 0.1980 chunk 60 optimal weight: 0.9990 chunk 301 optimal weight: 6.9990 chunk 287 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 279 optimal weight: 50.0000 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 387 ASN I 450 ASN I 811 ASN I1244 HIS J 651 HIS J 777 HIS J 865 HIS J 867 GLN J1326 GLN L 131 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.207259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.123525 restraints weight = 34409.218| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.37 r_work: 0.3177 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32085 Z= 0.129 Angle : 0.578 16.763 43761 Z= 0.301 Chirality : 0.042 0.346 5023 Planarity : 0.004 0.053 5344 Dihedral : 15.660 177.526 5428 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.08 % Allowed : 17.33 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.03 % 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: 0.30 (0.14), residues: 3704 helix: 1.82 (0.14), residues: 1486 sheet: -0.35 (0.24), residues: 451 loop : -1.09 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 388 TYR 0.016 0.001 TYR G 177 PHE 0.025 0.001 PHE L 165 TRP 0.008 0.001 TRP L 326 HIS 0.007 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (32077) covalent geometry : angle 0.57219 / 0.30 (43749) hydrogen bonds : bond 0.04152 / 2.88 ( 1415) hydrogen bonds : angle 4.22242 / 3.00 ( 3912) metal coordination : bond 0.00486 / 0.25 ( 8) metal coordination : angle 4.75278 / 2.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 368 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 67 GLU cc_start: 0.8177 (pt0) cc_final: 0.7874 (pm20) REVERT: G 80 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: G 125 LYS cc_start: 0.8657 (tttt) cc_final: 0.8382 (tttm) REVERT: G 129 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8269 (t) REVERT: G 186 ASN cc_start: 0.8569 (m-40) cc_final: 0.7998 (m110) REVERT: G 197 ASP cc_start: 0.7999 (p0) cc_final: 0.7618 (p0) REVERT: G 226 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7324 (pt0) REVERT: I 37 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7571 (mtpt) REVERT: I 88 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7859 (ttm170) REVERT: I 151 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8370 (ttm170) REVERT: I 197 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6583 (mtm-85) REVERT: I 203 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8329 (mtpm) REVERT: I 284 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.6919 (tm) REVERT: I 414 ILE cc_start: 0.8359 (tt) cc_final: 0.8135 (tt) REVERT: I 422 LYS cc_start: 0.7507 (ptmt) cc_final: 0.7274 (ptmt) REVERT: I 510 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: I 603 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8535 (mp) REVERT: I 642 SER cc_start: 0.8892 (p) cc_final: 0.8566 (t) REVERT: I 643 SER cc_start: 0.8346 (p) cc_final: 0.8047 (m) REVERT: I 672 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7887 (pm20) REVERT: I 699 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8455 (mp) REVERT: I 768 MET cc_start: 0.8972 (ptm) cc_final: 0.8733 (ptp) REVERT: I 876 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7882 (mp0) REVERT: I 916 SER cc_start: 0.8389 (t) cc_final: 0.7797 (p) REVERT: I 954 LYS cc_start: 0.7873 (mtpt) cc_final: 0.7514 (mttm) REVERT: I 1028 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7519 (tptm) REVERT: I 1082 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8376 (mt) REVERT: I 1090 ASN cc_start: 0.8281 (t0) cc_final: 0.7888 (m-40) REVERT: I 1188 ASP cc_start: 0.8857 (p0) cc_final: 0.8503 (p0) REVERT: I 1233 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8831 (mt) REVERT: I 1290 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8739 (mmt) REVERT: I 1319 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7750 (ttp) REVERT: J 66 LYS cc_start: 0.7417 (mtmm) cc_final: 0.6860 (pttm) REVERT: J 69 GLU cc_start: 0.8445 (pt0) cc_final: 0.8141 (pt0) REVERT: J 97 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8627 (m) REVERT: J 154 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5487 (mt) REVERT: J 158 GLN cc_start: 0.7922 (tt0) cc_final: 0.7417 (mt0) REVERT: J 227 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7106 (t80) REVERT: J 497 GLU cc_start: 0.8507 (mt-10) cc_final: 0.7859 (mm-30) REVERT: J 500 ILE cc_start: 0.8184 (mm) cc_final: 0.7954 (pt) REVERT: J 525 MET cc_start: 0.9072 (mtm) cc_final: 0.8757 (mtm) REVERT: J 603 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7941 (ttmm) REVERT: J 781 LYS cc_start: 0.8347 (tptm) cc_final: 0.7961 (ttmm) REVERT: J 788 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6855 (tm) REVERT: J 822 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.5433 (mpt) REVERT: J 1040 MET cc_start: 0.0453 (tpt) cc_final: -0.1970 (mtt) REVERT: J 1311 LYS cc_start: 0.7463 (tppp) cc_final: 0.7238 (ttmm) REVERT: J 1341 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7943 (ttt180) REVERT: J 1343 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6897 (mm-30) REVERT: J 1367 GLN cc_start: 0.7283 (mt0) cc_final: 0.6845 (mm110) REVERT: K 69 ARG cc_start: 0.7151 (tmm-80) cc_final: 0.6941 (tmm-80) REVERT: L 116 GLU cc_start: 0.7298 (mp0) cc_final: 0.7096 (mp0) REVERT: L 125 ASP cc_start: 0.9178 (t0) cc_final: 0.8934 (t0) REVERT: L 129 GLN cc_start: 0.9071 (mt0) cc_final: 0.8469 (mt0) REVERT: L 259 PHE cc_start: 0.7675 (m-80) cc_final: 0.7459 (m-80) REVERT: L 297 MET cc_start: 0.0028 (pmm) cc_final: -0.0436 (ppp) REVERT: L 395 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.7913 (m) REVERT: L 458 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7966 (tp30) REVERT: L 561 MET cc_start: 0.8148 (ttm) cc_final: 0.7352 (tmm) outliers start: 130 outliers final: 78 residues processed: 465 average time/residue: 0.6396 time to fit residues: 357.7807 Evaluate side-chains 465 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 360 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 197 ARG Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1028 LYS Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1089 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 568 SER Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 603 LYS Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1341 ARG Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain L residue 131 GLN Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 458 GLU Chi-restraints excluded: chain L residue 483 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 35 optimal weight: 0.9990 chunk 70 optimal weight: 0.0020 chunk 291 optimal weight: 50.0000 chunk 373 optimal weight: 50.0000 chunk 110 optimal weight: 0.9980 chunk 323 optimal weight: 50.0000 chunk 357 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 299 optimal weight: 0.9990 chunk 276 optimal weight: 6.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 387 ASN I 811 ASN I1244 HIS J 651 HIS J 777 HIS J 865 HIS J 867 GLN J1326 GLN L 131 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.207105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122794 restraints weight = 34440.110| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.22 r_work: 0.3181 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 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 0.051 32085 Z= 0.140 Angle : 0.587 17.070 43761 Z= 0.305 Chirality : 0.043 0.350 5023 Planarity : 0.004 0.055 5344 Dihedral : 15.620 177.474 5425 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.14 % Allowed : 17.55 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.03 % 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: 0.32 (0.14), residues: 3704 helix: 1.83 (0.14), residues: 1487 sheet: -0.31 (0.24), residues: 451 loop : -1.09 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 388 TYR 0.027 0.001 TYR J 144 PHE 0.027 0.001 PHE L 259 TRP 0.007 0.001 TRP L 326 HIS 0.007 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (32077) covalent geometry : angle 0.58143 / 0.30 (43749) hydrogen bonds : bond 0.04180 / 2.89 ( 1415) hydrogen bonds : angle 4.20693 / 2.99 ( 3912) metal coordination : bond 0.00493 / 0.26 ( 8) metal coordination : angle 4.70716 / 2.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 365 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 67 GLU cc_start: 0.8198 (pt0) cc_final: 0.7843 (pm20) REVERT: G 80 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: G 125 LYS cc_start: 0.8624 (tttt) cc_final: 0.8325 (tttm) REVERT: G 129 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8238 (t) REVERT: G 186 ASN cc_start: 0.8546 (m-40) cc_final: 0.7934 (m110) REVERT: G 197 ASP cc_start: 0.8018 (p0) cc_final: 0.7637 (p0) REVERT: G 226 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7196 (pt0) REVERT: I 37 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7564 (mtpt) REVERT: I 88 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7831 (ttm170) REVERT: I 151 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8344 (ttm170) REVERT: I 197 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.6501 (mtm-85) REVERT: I 203 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8291 (mtpm) REVERT: I 284 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.6910 (tm) REVERT: I 414 ILE cc_start: 0.8369 (tt) cc_final: 0.8137 (tt) REVERT: I 422 LYS cc_start: 0.7431 (ptmt) cc_final: 0.7178 (ptmt) REVERT: I 510 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: I 603 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8548 (mp) REVERT: I 642 SER cc_start: 0.8905 (p) cc_final: 0.8548 (t) REVERT: I 643 SER cc_start: 0.8299 (p) cc_final: 0.7989 (m) REVERT: I 672 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.7881 (pm20) REVERT: I 699 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8460 (mp) REVERT: I 768 MET cc_start: 0.8955 (ptm) cc_final: 0.8705 (ptp) REVERT: I 876 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7824 (mp0) REVERT: I 916 SER cc_start: 0.8368 (t) cc_final: 0.7757 (p) REVERT: I 954 LYS cc_start: 0.7800 (mtpt) cc_final: 0.7430 (mttm) REVERT: I 1028 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7557 (tptm) REVERT: I 1082 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8334 (mt) REVERT: I 1090 ASN cc_start: 0.8197 (t0) cc_final: 0.7813 (m-40) REVERT: I 1188 ASP cc_start: 0.8805 (p0) cc_final: 0.8471 (p0) REVERT: I 1233 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8833 (mt) REVERT: I 1290 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8764 (mmt) REVERT: I 1319 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7769 (ttp) REVERT: J 66 LYS cc_start: 0.7358 (mtmm) cc_final: 0.6791 (pttm) REVERT: J 69 GLU cc_start: 0.8426 (pt0) cc_final: 0.8107 (pt0) REVERT: J 97 VAL cc_start: 0.8914 (OUTLIER) cc_final: 0.8597 (m) REVERT: J 154 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5487 (mt) REVERT: J 158 GLN cc_start: 0.7874 (tt0) cc_final: 0.7368 (mt0) REVERT: J 227 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7002 (t80) REVERT: J 497 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8024 (mm-30) REVERT: J 500 ILE cc_start: 0.8219 (mm) cc_final: 0.7955 (pt) REVERT: J 525 MET cc_start: 0.9085 (mtm) cc_final: 0.8749 (mtm) REVERT: J 603 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7924 (ttmm) REVERT: J 781 LYS cc_start: 0.8294 (tptm) cc_final: 0.7870 (ttmm) REVERT: J 788 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6769 (tm) REVERT: J 822 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.5363 (mpt) REVERT: J 1040 MET cc_start: 0.0438 (tpt) cc_final: -0.1980 (mtt) REVERT: J 1311 LYS cc_start: 0.7465 (tppp) cc_final: 0.7231 (ttmm) REVERT: J 1341 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7924 (ttt180) REVERT: J 1343 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6876 (mm-30) REVERT: J 1367 GLN cc_start: 0.7181 (mt0) cc_final: 0.6724 (mm110) REVERT: K 69 ARG cc_start: 0.7100 (tmm-80) cc_final: 0.6880 (tmm-80) REVERT: L 125 ASP cc_start: 0.9186 (t0) cc_final: 0.8885 (t0) REVERT: L 297 MET cc_start: -0.0051 (pmm) cc_final: -0.0438 (ppp) REVERT: L 395 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.7923 (m) REVERT: L 458 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7899 (tp30) REVERT: L 561 MET cc_start: 0.8129 (ttm) cc_final: 0.7324 (tmm) outliers start: 132 outliers final: 85 residues processed: 460 average time/residue: 0.5753 time to fit residues: 317.6926 Evaluate side-chains 467 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 355 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 197 ARG Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1028 LYS Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1089 GLU Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 320 ASN Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 568 SER Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 603 LYS Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1255 VAL Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1341 ARG Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain L residue 131 GLN Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 458 GLU Chi-restraints excluded: chain L residue 474 MET Chi-restraints excluded: chain L residue 483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 162 optimal weight: 0.9980 chunk 154 optimal weight: 0.0000 chunk 240 optimal weight: 0.1980 chunk 202 optimal weight: 0.9980 chunk 226 optimal weight: 0.9980 chunk 374 optimal weight: 50.0000 chunk 318 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 69 optimal weight: 0.0170 chunk 143 optimal weight: 30.0000 chunk 132 optimal weight: 0.6980 overall best weight: 0.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 387 ASN I 811 ASN I1244 HIS J 651 HIS J 777 HIS J 867 GLN J1326 GLN L 131 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.208497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.125186 restraints weight = 34503.238| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.23 r_work: 0.3215 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 32085 Z= 0.115 Angle : 0.576 17.471 43761 Z= 0.299 Chirality : 0.042 0.337 5023 Planarity : 0.004 0.050 5344 Dihedral : 15.575 177.451 5425 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.30 % Allowed : 18.74 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.03 % 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: 0.42 (0.14), residues: 3704 helix: 1.92 (0.14), residues: 1486 sheet: -0.21 (0.25), residues: 459 loop : -1.06 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 388 TYR 0.029 0.001 TYR J 144 PHE 0.026 0.001 PHE L 259 TRP 0.007 0.001 TRP L 326 HIS 0.005 0.001 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (32077) covalent geometry : angle 0.57072 / 0.30 (43749) hydrogen bonds : bond 0.03840 / 2.65 ( 1415) hydrogen bonds : angle 4.16932 / 2.97 ( 3912) metal coordination : bond 0.00439 / 0.22 ( 8) metal coordination : angle 4.53697 / 2.73 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 375 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 67 GLU cc_start: 0.8137 (pt0) cc_final: 0.7813 (pt0) REVERT: G 80 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: G 125 LYS cc_start: 0.8609 (tttt) cc_final: 0.8328 (tttm) REVERT: G 129 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8189 (t) REVERT: G 139 SER cc_start: 0.9191 (p) cc_final: 0.8759 (m) REVERT: G 186 ASN cc_start: 0.8539 (m-40) cc_final: 0.7931 (m110) REVERT: G 197 ASP cc_start: 0.7992 (p0) cc_final: 0.7635 (p0) REVERT: G 226 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7173 (pt0) REVERT: I 88 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7801 (ttm170) REVERT: I 151 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8307 (ttm170) REVERT: I 197 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6559 (mtm-85) REVERT: I 203 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8286 (mtpm) REVERT: I 284 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.6973 (tm) REVERT: I 414 ILE cc_start: 0.8372 (tt) cc_final: 0.8146 (tt) REVERT: I 603 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8517 (mp) REVERT: I 672 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.7847 (pm20) REVERT: I 699 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8552 (mp) REVERT: I 866 ASP cc_start: 0.7776 (p0) cc_final: 0.7384 (p0) REVERT: I 876 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7789 (mp0) REVERT: I 916 SER cc_start: 0.8322 (t) cc_final: 0.7860 (p) REVERT: I 954 LYS cc_start: 0.7826 (mtpt) cc_final: 0.7459 (mttm) REVERT: I 1028 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7549 (tptm) REVERT: I 1090 ASN cc_start: 0.8125 (t0) cc_final: 0.7721 (m-40) REVERT: I 1188 ASP cc_start: 0.8759 (p0) cc_final: 0.8441 (p0) REVERT: I 1203 ASP cc_start: 0.7207 (m-30) cc_final: 0.6985 (m-30) REVERT: I 1290 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8732 (mmt) REVERT: I 1319 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7624 (ttp) REVERT: J 66 LYS cc_start: 0.7331 (mtmm) cc_final: 0.6825 (pttm) REVERT: J 69 GLU cc_start: 0.8361 (pt0) cc_final: 0.8113 (pt0) REVERT: J 97 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8611 (m) REVERT: J 154 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.5540 (mt) REVERT: J 227 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7003 (t80) REVERT: J 497 GLU cc_start: 0.8516 (mt-10) cc_final: 0.7909 (mm-30) REVERT: J 525 MET cc_start: 0.9065 (mtm) cc_final: 0.8749 (mtm) REVERT: J 603 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7900 (ttmm) REVERT: J 781 LYS cc_start: 0.8286 (tptm) cc_final: 0.7871 (ttmm) REVERT: J 788 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6722 (tm) REVERT: J 822 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.5471 (mpt) REVERT: J 1040 MET cc_start: 0.0392 (tpt) cc_final: -0.2025 (mtt) REVERT: J 1311 LYS cc_start: 0.7451 (tppp) cc_final: 0.7220 (ttmm) REVERT: J 1343 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.7016 (mm-30) REVERT: J 1367 GLN cc_start: 0.7184 (mt0) cc_final: 0.6773 (mm110) REVERT: K 69 ARG cc_start: 0.7170 (tmm-80) cc_final: 0.6943 (tmm-80) REVERT: L 125 ASP cc_start: 0.9138 (t0) cc_final: 0.8832 (t0) REVERT: L 297 MET cc_start: -0.0031 (pmm) cc_final: -0.0405 (ppp) REVERT: L 395 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7855 (m) REVERT: L 458 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7906 (tp30) REVERT: L 561 MET cc_start: 0.8124 (ttm) cc_final: 0.7343 (tmm) outliers start: 105 outliers final: 69 residues processed: 449 average time/residue: 0.6343 time to fit residues: 343.2987 Evaluate side-chains 445 residues out of total 3203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 354 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 160 HIS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 197 ARG Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 445 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 513 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 893 THR Chi-restraints excluded: chain I residue 905 ILE Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1028 LYS Chi-restraints excluded: chain I residue 1046 VAL Chi-restraints excluded: chain I residue 1089 GLU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1319 MET Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 568 SER Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 603 LYS Chi-restraints excluded: chain J residue 649 LYS Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 822 MET Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1368 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain L residue 131 GLN Chi-restraints excluded: chain L residue 259 PHE Chi-restraints excluded: chain L residue 395 THR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 458 GLU Chi-restraints excluded: chain L residue 483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 212 optimal weight: 0.8980 chunk 121 optimal weight: 0.0010 chunk 274 optimal weight: 30.0000 chunk 256 optimal weight: 4.9990 chunk 172 optimal weight: 0.5980 chunk 361 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 387 ASN I 811 ASN I1244 HIS J 651 HIS J 777 HIS J 867 GLN J1326 GLN L 131 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.207803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122926 restraints weight = 34469.879| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.18 r_work: 0.3162 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32085 Z= 0.134 Angle : 0.588 17.167 43761 Z= 0.305 Chirality : 0.042 0.346 5023 Planarity : 0.004 0.053 5344 Dihedral : 15.569 177.408 5423 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.26 % Allowed : 18.93 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.03 % 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: 0.40 (0.14), residues: 3704 helix: 1.90 (0.14), residues: 1480 sheet: -0.20 (0.25), residues: 459 loop : -1.06 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 388 TYR 0.028 0.001 TYR J 144 PHE 0.025 0.001 PHE L 266 TRP 0.007 0.001 TRP L 326 HIS 0.005 0.001 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (32077) covalent geometry : angle 0.58341 / 0.30 (43749) hydrogen bonds : bond 0.03960 / 2.75 ( 1415) hydrogen bonds : angle 4.17026 / 2.97 ( 3912) metal coordination : bond 0.00470 / 0.25 ( 8) metal coordination : angle 4.55771 / 2.74 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15545.26 seconds wall clock time: 263 minutes 46.96 seconds (15826.96 seconds total)