Starting phenix.real_space_refine on Mon Sep 14 01:09:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g2w_29683/09_2026/8g2w_29683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g2w_29683/09_2026/8g2w_29683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g2w_29683/09_2026/8g2w_29683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g2w_29683/09_2026/8g2w_29683.map" model { file = "/net/cci-nas-00/data/ceres_data/8g2w_29683/09_2026/8g2w_29683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g2w_29683/09_2026/8g2w_29683.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8g2w_29683/09_2026/8g2w_29683.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g2w_29683/09_2026/8g2w_29683.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 94 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16495 2.51 5 N 4755 2.21 5 O 5378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.20s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26829 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 388 Inner-chain residues flagged as termini: ['pdbres=" DG A 25 "'] Classifications: {'DNA': 19} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 18} Chain: "B" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 631 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "G" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1708 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 1 Chain: "H" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1693 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10381 Classifications: {'peptide': 1316} Link IDs: {'PTRANS': 55, 'TRANS': 1260} Chain breaks: 1 Chain: "J" Number of atoms: 10403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10403 Classifications: {'peptide': 1337} Link IDs: {'PTRANS': 55, 'TRANS': 1281} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 997 Classifications: {'RNAv2': 47} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 11, 'rna3p': 35} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.47, per 1000 atoms: 0.20 Number of scatterers: 26829 At special positions: 0 Unit cell: (135, 157, 161, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 106 16.00 P 94 15.00 Mg 1 11.99 O 5378 8.00 N 4755 7.00 C 16495 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: 2.05 Conformation dependent library (CDL) restraints added in 1.0 seconds 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 41 sheets defined 39.4% alpha, 15.6% beta 32 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 Processing helix chain 'G' and resid 77 through 88 Processing helix chain 'G' and resid 212 through 232 removed outlier: 3.607A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.642A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 212 through 228 Processing helix chain 'H' and resid 228 through 233 removed outlier: 3.545A pdb=" N VAL H 232 " --> pdb=" O LEU H 228 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP H 233 " --> pdb=" O GLU H 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 228 through 233' Processing helix chain 'I' and resid 4 through 10 Processing helix chain 'I' and resid 28 through 40 Processing helix chain 'I' and resid 48 through 56 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.202A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 4.028A pdb=" N LEU I 246 " --> pdb=" O VAL I 242 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG I 247 " --> pdb=" O PRO I 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 242 through 247' Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 295 removed outlier: 3.833A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 329 Processing helix chain 'I' and resid 345 through 354 removed outlier: 3.578A 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 390 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 482 Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.597A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 529 Processing helix chain 'I' and resid 544 through 549 removed outlier: 3.550A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 608 through 614 removed outlier: 3.743A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 614' Processing helix chain 'I' and resid 662 through 667 removed outlier: 3.553A pdb=" N LEU I 667 " --> pdb=" O VAL I 663 " (cutoff:3.500A) Processing helix chain 'I' and resid 675 through 688 removed outlier: 3.758A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 865 removed outlier: 3.775A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU I 865 " --> pdb=" O ALA I 861 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 977 Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.611A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS I 991 " --> pdb=" O GLU I 987 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 3.866A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.536A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 removed outlier: 3.615A pdb=" N LYS I1242 " --> pdb=" O LEU I1238 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1333 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 95 through 101 removed outlier: 3.762A pdb=" N ARG J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU J 100 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 119 removed outlier: 3.554A 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 162 through 172 Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 255 through 259 Processing helix chain 'J' and resid 264 through 286 removed outlier: 3.830A pdb=" N LEU J 268 " --> pdb=" O ASP J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 318 through 322 removed outlier: 3.535A pdb=" N LYS J 321 " --> pdb=" O GLY J 318 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG J 322 " --> pdb=" O SER J 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 318 through 322' Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 418 removed outlier: 3.720A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU J 418 " --> pdb=" O GLU J 414 " (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 458 removed outlier: 4.037A pdb=" N ALA J 455 " --> pdb=" O PRO J 451 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA J 456 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 540 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.881A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 594 removed outlier: 3.851A pdb=" N GLN J 594 " --> pdb=" O SER J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 613 through 636 Processing helix chain 'J' and resid 647 through 670 removed outlier: 4.426A pdb=" N HIS J 651 " --> pdb=" O PRO J 647 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.612A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 895 through 900 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.619A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1068 through 1074 removed outlier: 4.355A pdb=" N LEU J1074 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 removed outlier: 3.599A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 4.036A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 3.981A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.735A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 Processing helix chain 'J' and resid 1361 through 1373 removed outlier: 4.074A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 33 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 80 removed outlier: 3.514A pdb=" N GLU K 79 " --> pdb=" O GLN K 75 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 17 removed outlier: 4.005A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (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: 3.830A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.941A 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: 3.556A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 15 through 18 removed outlier: 4.611A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR H 27 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU H 198 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA H 189 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS H 200 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL H 187 " --> pdb=" O LYS H 200 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL H 202 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 99 through 105 removed outlier: 3.699A pdb=" N LEU H 102 " --> pdb=" O MET H 142 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.967A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) 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: 6.359A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 66 through 75 removed outlier: 3.757A pdb=" N VAL I 71 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (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: 6.414A 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 158 Processing sheet with id=AB7, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB8, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.703A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.917A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.541A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.612A pdb=" N ASP I 654 " --> pdb=" O ALA I 617 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE I 616 " --> pdb=" O ARG I 637 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 717 removed outlier: 7.128A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 750 through 752 removed outlier: 6.916A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN I 725 " --> pdb=" O VAL I 733 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 3.580A pdb=" N VAL I1225 " --> pdb=" O ILE I1210 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.717A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.717A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.991A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD3, first strand: chain 'I' and resid 1335 through 1338 Processing sheet with id=AD4, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.626A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.056A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 143 through 145 Processing sheet with id=AD6, first strand: chain 'J' and resid 350 through 356 removed outlier: 7.412A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER J 353 " --> pdb=" O MET J 466 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 547 through 556 Processing sheet with id=AD8, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD9, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.953A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.505A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 1024 through 1025 removed outlier: 3.506A pdb=" N ILE J1124 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE J1106 " --> pdb=" O ARG J1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id=AE4, first strand: chain 'J' and resid 1186 through 1190 removed outlier: 4.325A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE J1177 " --> pdb=" O TYR J1186 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1279 through 1281 1072 hydrogen bonds defined for protein. 3063 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 8.38 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7333 1.33 - 1.45: 4479 1.45 - 1.57: 15249 1.57 - 1.69: 187 1.69 - 1.81: 184 Bond restraints: 27432 Sorted by residual: bond pdb=" C ALA J 459 " pdb=" N ASP J 460 " ideal model delta sigma weight residual 1.330 1.434 -0.104 1.60e-02 3.91e+03 4.24e+01 bond pdb=" C1' DC A 13 " pdb=" N1 DC A 13 " ideal model delta sigma weight residual 1.468 1.544 -0.076 1.40e-02 5.10e+03 2.95e+01 bond pdb=" O3' DC B 3 " pdb=" P DT B 4 " ideal model delta sigma weight residual 1.607 1.667 -0.060 1.20e-02 6.94e+03 2.54e+01 bond pdb=" O3' DC B 17 " pdb=" P DG B 18 " ideal model delta sigma weight residual 1.607 1.664 -0.057 1.20e-02 6.94e+03 2.29e+01 bond pdb=" O3' DG B 5 " pdb=" P DA B 6 " ideal model delta sigma weight residual 1.607 1.652 -0.045 1.20e-02 6.94e+03 1.43e+01 ... (remaining 27427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 36753 2.16 - 4.31: 652 4.31 - 6.47: 71 6.47 - 8.62: 9 8.62 - 10.78: 2 Bond angle restraints: 37487 Sorted by residual: angle pdb=" N ASP J 806 " pdb=" CA ASP J 806 " pdb=" C ASP J 806 " ideal model delta sigma weight residual 112.59 105.37 7.22 1.22e+00 6.72e-01 3.50e+01 angle pdb=" O ALA J 459 " pdb=" C ALA J 459 " pdb=" N ASP J 460 " ideal model delta sigma weight residual 123.29 130.19 -6.90 1.18e+00 7.18e-01 3.42e+01 angle pdb=" N ALA I1263 " pdb=" CA ALA I1263 " pdb=" C ALA I1263 " ideal model delta sigma weight residual 111.28 105.52 5.76 1.09e+00 8.42e-01 2.79e+01 angle pdb=" N VAL J 803 " pdb=" CA VAL J 803 " pdb=" C VAL J 803 " ideal model delta sigma weight residual 111.09 104.77 6.32 1.25e+00 6.40e-01 2.56e+01 angle pdb=" N ARG J 259 " pdb=" CA ARG J 259 " pdb=" C ARG J 259 " ideal model delta sigma weight residual 111.28 105.90 5.38 1.09e+00 8.42e-01 2.43e+01 ... (remaining 37482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 15985 35.88 - 71.76: 589 71.76 - 107.64: 42 107.64 - 143.52: 3 143.52 - 179.40: 2 Dihedral angle restraints: 16621 sinusoidal: 7518 harmonic: 9103 Sorted by residual: dihedral pdb=" C4' U R 24 " pdb=" C3' U R 24 " pdb=" C2' U R 24 " pdb=" C1' U R 24 " ideal model delta sinusoidal sigma weight residual 36.35 -36.28 72.62 1 3.10e+00 1.04e-01 7.01e+02 dihedral pdb=" C4' U R 26 " pdb=" C3' U R 26 " pdb=" C2' U R 26 " pdb=" C1' U R 26 " ideal model delta sinusoidal sigma weight residual 36.35 -35.94 72.28 1 3.10e+00 1.04e-01 6.95e+02 dihedral pdb=" C4' G R 1 " pdb=" C3' G R 1 " pdb=" C2' G R 1 " pdb=" C1' G R 1 " ideal model delta sinusoidal sigma weight residual 36.34 -35.73 72.07 1 3.10e+00 1.04e-01 6.91e+02 ... (remaining 16618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4025 0.094 - 0.189: 213 0.189 - 0.283: 73 0.283 - 0.377: 4 0.377 - 0.471: 2 Chirality restraints: 4317 Sorted by residual: chirality pdb=" P G R 38 " pdb=" OP1 G R 38 " pdb=" OP2 G R 38 " pdb=" O5' G R 38 " both_signs ideal model delta sigma weight residual True 2.17 -2.64 -0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" P G R 37 " pdb=" OP1 G R 37 " pdb=" OP2 G R 37 " pdb=" O5' G R 37 " both_signs ideal model delta sigma weight residual True 2.17 -2.64 -0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" P A R 3 " pdb=" OP1 A R 3 " pdb=" OP2 A R 3 " pdb=" O5' A R 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.52 -0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 4314 not shown) Planarity restraints: 4558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP J 460 " 0.015 2.00e-02 2.50e+03 3.13e-02 9.77e+00 pdb=" C ASP J 460 " -0.054 2.00e-02 2.50e+03 pdb=" O ASP J 460 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE J 461 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 804 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.10e+00 pdb=" C ALA J 804 " -0.049 2.00e-02 2.50e+03 pdb=" O ALA J 804 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN J 805 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS J 749 " 0.037 5.00e-02 4.00e+02 5.54e-02 4.90e+00 pdb=" N PRO J 750 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO J 750 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO J 750 " 0.031 5.00e-02 4.00e+02 ... (remaining 4555 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 338 2.61 - 3.18: 24245 3.18 - 3.76: 44515 3.76 - 4.33: 60715 4.33 - 4.90: 97090 Nonbonded interactions: 226903 Sorted by model distance: nonbonded pdb=" CB ALA J 108 " pdb=" CD2 LEU J 279 " model vdw 2.039 3.880 nonbonded pdb=" O ASP J 462 " pdb=" OD1 ASP J 462 " model vdw 2.085 3.040 nonbonded pdb=" CB TYR I1251 " pdb=" OE1 GLN I1257 " model vdw 2.096 3.440 nonbonded pdb=" OG1 THR H 22 " pdb=" O THR H 207 " model vdw 2.101 3.040 nonbonded pdb=" OG SER I 391 " pdb=" OD1 ASP I 393 " model vdw 2.108 3.040 ... (remaining 226898 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 8 through 158 or resid 170 through 234)) selection = (chain 'H' and resid 8 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 28.750 Find NCS groups from input model: 0.310 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: 0.010 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 27432 Z= 0.228 Angle : 0.667 10.780 37487 Z= 0.396 Chirality : 0.054 0.471 4317 Planarity : 0.004 0.055 4558 Dihedral : 17.323 179.396 10765 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.38 % Favored : 97.59 % Rotamer: Outliers : 0.11 % Allowed : 0.37 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.15), residues: 3152 helix: 1.84 (0.15), residues: 1105 sheet: 1.00 (0.25), residues: 425 loop : 0.28 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 779 TYR 0.015 0.001 TYR J 631 PHE 0.018 0.001 PHE J 461 TRP 0.008 0.001 TRP I 183 HIS 0.007 0.001 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.23 (27432) covalent geometry : angle 0.66743 / 0.40 (37487) hydrogen bonds : bond 0.17679 / 19.38 ( 1140) hydrogen bonds : angle 7.10663 / 6.73 ( 3221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 704 time to evaluate : 1.004 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 156 SER cc_start: 0.9373 (p) cc_final: 0.9022 (t) REVERT: G 185 TYR cc_start: 0.8934 (p90) cc_final: 0.8626 (p90) REVERT: H 32 GLU cc_start: 0.7298 (tp30) cc_final: 0.6701 (mm-30) REVERT: H 131 CYS cc_start: 0.7348 (p) cc_final: 0.5776 (p) REVERT: H 185 TYR cc_start: 0.8631 (p90) cc_final: 0.8386 (p90) REVERT: I 142 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7764 (mt-10) REVERT: I 454 ARG cc_start: 0.8873 (ttm170) cc_final: 0.8657 (ttp80) REVERT: I 516 ASP cc_start: 0.6817 (p0) cc_final: 0.6216 (p0) REVERT: I 768 MET cc_start: 0.7169 (ttt) cc_final: 0.6911 (ttt) REVERT: I 785 ASP cc_start: 0.6463 (m-30) cc_final: 0.6046 (p0) REVERT: I 788 SER cc_start: 0.9129 (m) cc_final: 0.8740 (p) REVERT: I 1066 MET cc_start: 0.8375 (tpp) cc_final: 0.8047 (tpp) REVERT: I 1085 MET cc_start: 0.9055 (mmm) cc_final: 0.8728 (mmm) REVERT: I 1117 LEU cc_start: 0.9401 (tp) cc_final: 0.9178 (tp) REVERT: J 96 LYS cc_start: 0.8373 (ttmt) cc_final: 0.8044 (mtpt) REVERT: J 97 VAL cc_start: 0.7773 (t) cc_final: 0.7065 (t) REVERT: J 100 GLU cc_start: 0.8109 (mp0) cc_final: 0.7613 (mp0) REVERT: J 197 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7947 (mt-10) REVERT: J 249 LEU cc_start: 0.9212 (mt) cc_final: 0.9003 (mt) REVERT: J 301 GLU cc_start: 0.8624 (tp30) cc_final: 0.8249 (tm-30) REVERT: J 342 LEU cc_start: 0.9463 (mp) cc_final: 0.9246 (mp) REVERT: J 398 LYS cc_start: 0.8366 (mttt) cc_final: 0.8049 (mttp) REVERT: J 429 LEU cc_start: 0.9123 (mt) cc_final: 0.8894 (mp) REVERT: J 445 LYS cc_start: 0.8385 (mttt) cc_final: 0.8023 (mttt) REVERT: J 470 VAL cc_start: 0.9227 (t) cc_final: 0.9007 (t) REVERT: J 484 MET cc_start: 0.8682 (mmm) cc_final: 0.8308 (mmm) REVERT: J 723 TYR cc_start: 0.8745 (t80) cc_final: 0.8517 (t80) REVERT: J 835 LEU cc_start: 0.8506 (tp) cc_final: 0.8288 (tp) REVERT: J 836 ARG cc_start: 0.8067 (tmm160) cc_final: 0.7452 (ttp80) REVERT: J 1123 ARG cc_start: 0.8480 (mtt180) cc_final: 0.8085 (mtp85) REVERT: J 1189 MET cc_start: 0.7331 (tpt) cc_final: 0.6995 (mmt) REVERT: J 1208 ASP cc_start: 0.7443 (m-30) cc_final: 0.7170 (m-30) REVERT: J 1250 ASP cc_start: 0.8517 (m-30) cc_final: 0.8291 (m-30) REVERT: J 1254 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7815 (mt-10) REVERT: K 55 GLU cc_start: 0.8468 (tt0) cc_final: 0.8124 (tt0) outliers start: 3 outliers final: 0 residues processed: 706 average time/residue: 0.2080 time to fit residues: 222.4683 Evaluate side-chains 341 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.0170 chunk 298 optimal weight: 6.9990 overall best weight: 2.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 23 HIS G 41 ASN H 194 GLN I 46 GLN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 684 ASN I 799 ASN I 808 ASN I 811 ASN ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS I1264 GLN ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 921 GLN J1195 GLN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.117437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.089274 restraints weight = 74325.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.092077 restraints weight = 35201.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.093883 restraints weight = 22173.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.094983 restraints weight = 16816.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.095618 restraints weight = 14378.629| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 27432 Z= 0.223 Angle : 0.878 19.576 37487 Z= 0.415 Chirality : 0.070 1.098 4317 Planarity : 0.005 0.057 4558 Dihedral : 15.121 174.128 4562 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.26 % Allowed : 13.37 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.14), residues: 3152 helix: 1.41 (0.15), residues: 1142 sheet: 0.86 (0.25), residues: 419 loop : 0.13 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 978 TYR 0.034 0.002 TYR I1229 PHE 0.020 0.002 PHE J 988 TRP 0.013 0.002 TRP J 580 HIS 0.012 0.002 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 (27432) covalent geometry : angle 0.87837 / 0.41 (37487) hydrogen bonds : bond 0.05097 / 5.67 ( 1140) hydrogen bonds : angle 5.56951 / 5.63 ( 3221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 389 time to evaluate : 1.102 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: G 156 SER cc_start: 0.9407 (p) cc_final: 0.9120 (t) REVERT: H 29 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6861 (mm-30) REVERT: H 32 GLU cc_start: 0.7387 (tp30) cc_final: 0.7016 (mm-30) REVERT: H 131 CYS cc_start: 0.7124 (p) cc_final: 0.6322 (p) REVERT: H 185 TYR cc_start: 0.8904 (p90) cc_final: 0.8602 (p90) REVERT: I 116 ASP cc_start: 0.6732 (p0) cc_final: 0.6366 (t70) REVERT: I 142 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7684 (mt-10) REVERT: I 414 ILE cc_start: 0.9181 (mm) cc_final: 0.8625 (tp) REVERT: I 516 ASP cc_start: 0.7419 (p0) cc_final: 0.6633 (p0) REVERT: I 788 SER cc_start: 0.9175 (m) cc_final: 0.8815 (p) REVERT: I 798 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7002 (mm-40) REVERT: I 811 ASN cc_start: 0.9253 (OUTLIER) cc_final: 0.9008 (p0) REVERT: I 1085 MET cc_start: 0.9154 (mmm) cc_final: 0.8724 (mmm) REVERT: I 1117 LEU cc_start: 0.9465 (tp) cc_final: 0.9254 (tp) REVERT: I 1229 TYR cc_start: 0.9031 (m-80) cc_final: 0.8643 (m-10) REVERT: I 1273 MET cc_start: 0.8469 (mtp) cc_final: 0.8012 (mtt) REVERT: J 96 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7882 (mtpt) REVERT: J 97 VAL cc_start: 0.7579 (t) cc_final: 0.6960 (t) REVERT: J 100 GLU cc_start: 0.8220 (mp0) cc_final: 0.7597 (mp0) REVERT: J 137 ARG cc_start: 0.8495 (mtp-110) cc_final: 0.8006 (ptp90) REVERT: J 199 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8180 (pm20) REVERT: J 301 GLU cc_start: 0.8606 (tp30) cc_final: 0.8235 (tm-30) REVERT: J 418 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7139 (mm-30) REVERT: J 466 MET cc_start: 0.8189 (mtm) cc_final: 0.7944 (mtt) REVERT: J 497 GLU cc_start: 0.7873 (mp0) cc_final: 0.7601 (pm20) REVERT: J 504 GLN cc_start: 0.7730 (mp10) cc_final: 0.7309 (mp10) REVERT: J 532 GLU cc_start: 0.8213 (tt0) cc_final: 0.8002 (tt0) REVERT: J 656 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7637 (mt-10) REVERT: J 723 TYR cc_start: 0.8871 (t80) cc_final: 0.8648 (t80) REVERT: J 835 LEU cc_start: 0.8343 (tp) cc_final: 0.8077 (tp) REVERT: J 1123 ARG cc_start: 0.8282 (mtt180) cc_final: 0.7918 (mtp-110) REVERT: J 1250 ASP cc_start: 0.8612 (m-30) cc_final: 0.8372 (m-30) REVERT: J 1254 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8046 (mt-10) REVERT: K 11 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8149 (pm20) REVERT: K 43 ASN cc_start: 0.8957 (t0) cc_final: 0.8555 (t0) outliers start: 61 outliers final: 37 residues processed: 429 average time/residue: 0.1755 time to fit residues: 120.4160 Evaluate side-chains 361 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 321 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 692 THR Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 619 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 978 ARG Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 258 optimal weight: 0.5980 chunk 301 optimal weight: 0.0770 chunk 45 optimal weight: 8.9990 chunk 221 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 222 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 450 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 628 HIS I 766 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS I1256 GLN ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 232 ASN ** J 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1235 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.110045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.082158 restraints weight = 71470.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.084627 restraints weight = 36850.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.086194 restraints weight = 24027.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.087251 restraints weight = 18476.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.087884 restraints weight = 15846.099| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27432 Z= 0.155 Angle : 0.707 13.744 37487 Z= 0.346 Chirality : 0.054 0.937 4317 Planarity : 0.004 0.055 4558 Dihedral : 15.089 176.108 4562 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.44 % Favored : 97.53 % Rotamer: Outliers : 2.55 % Allowed : 15.70 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.14), residues: 3152 helix: 1.39 (0.15), residues: 1140 sheet: 0.77 (0.26), residues: 397 loop : -0.01 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 978 TYR 0.035 0.002 TYR H 177 PHE 0.024 0.002 PHE I1025 TRP 0.014 0.002 TRP J 580 HIS 0.013 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (27432) covalent geometry : angle 0.70699 / 0.35 (37487) hydrogen bonds : bond 0.04558 / 5.07 ( 1140) hydrogen bonds : angle 5.20611 / 5.28 ( 3221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 375 time to evaluate : 1.003 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: G 35 PHE cc_start: 0.7734 (m-80) cc_final: 0.7465 (m-80) REVERT: G 185 TYR cc_start: 0.8782 (p90) cc_final: 0.8538 (p90) REVERT: H 185 TYR cc_start: 0.8825 (p90) cc_final: 0.8532 (p90) REVERT: I 116 ASP cc_start: 0.6209 (p0) cc_final: 0.5919 (t70) REVERT: I 142 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7636 (mt-10) REVERT: I 193 ASN cc_start: 0.7972 (m-40) cc_final: 0.7707 (t0) REVERT: I 369 MET cc_start: 0.8158 (tmm) cc_final: 0.7661 (tmm) REVERT: I 422 LYS cc_start: 0.7151 (mptt) cc_final: 0.6544 (mptt) REVERT: I 516 ASP cc_start: 0.7299 (p0) cc_final: 0.6403 (p0) REVERT: I 788 SER cc_start: 0.9042 (m) cc_final: 0.8660 (p) REVERT: I 798 GLN cc_start: 0.7586 (mm-40) cc_final: 0.7092 (mm-40) REVERT: I 1040 ASP cc_start: 0.6469 (t70) cc_final: 0.6201 (t70) REVERT: I 1085 MET cc_start: 0.9022 (mmm) cc_final: 0.8640 (mmm) REVERT: I 1273 MET cc_start: 0.8254 (mtp) cc_final: 0.7905 (mtt) REVERT: I 1339 LEU cc_start: 0.8606 (mp) cc_final: 0.8388 (mt) REVERT: J 96 LYS cc_start: 0.8286 (ttmt) cc_final: 0.7927 (mtpt) REVERT: J 97 VAL cc_start: 0.7614 (t) cc_final: 0.7013 (t) REVERT: J 100 GLU cc_start: 0.8099 (mp0) cc_final: 0.7595 (mp0) REVERT: J 137 ARG cc_start: 0.8424 (mtp-110) cc_final: 0.8114 (ptp90) REVERT: J 301 GLU cc_start: 0.8653 (tp30) cc_final: 0.8266 (tm-30) REVERT: J 466 MET cc_start: 0.7954 (mtm) cc_final: 0.7739 (mtt) REVERT: J 484 MET cc_start: 0.8754 (mmm) cc_final: 0.8398 (mmp) REVERT: J 497 GLU cc_start: 0.7553 (mp0) cc_final: 0.7348 (mp0) REVERT: J 504 GLN cc_start: 0.7616 (mp10) cc_final: 0.7302 (mp10) REVERT: J 697 MET cc_start: 0.8055 (ttp) cc_final: 0.7726 (ttp) REVERT: J 1123 ARG cc_start: 0.8185 (mtt180) cc_final: 0.7916 (mtp-110) REVERT: J 1254 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7752 (mt-10) REVERT: K 43 ASN cc_start: 0.8998 (t0) cc_final: 0.8714 (t0) outliers start: 69 outliers final: 39 residues processed: 418 average time/residue: 0.1577 time to fit residues: 106.9215 Evaluate side-chains 354 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 315 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 191 ARG Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 202 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 HIS I 490 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS I1256 GLN ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.108290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.080105 restraints weight = 71924.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.082490 restraints weight = 37788.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.084098 restraints weight = 24946.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.085074 restraints weight = 19213.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.085625 restraints weight = 16525.542| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27432 Z= 0.196 Angle : 0.701 13.566 37487 Z= 0.346 Chirality : 0.051 0.683 4317 Planarity : 0.004 0.054 4558 Dihedral : 15.019 174.709 4562 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.18 % Allowed : 16.85 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.14), residues: 3152 helix: 1.35 (0.15), residues: 1147 sheet: 0.67 (0.26), residues: 395 loop : -0.12 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 220 TYR 0.043 0.002 TYR I1229 PHE 0.029 0.002 PHE I1025 TRP 0.016 0.002 TRP I1276 HIS 0.015 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (27432) covalent geometry : angle 0.70124 / 0.35 (37487) hydrogen bonds : bond 0.04370 / 4.84 ( 1140) hydrogen bonds : angle 5.11610 / 5.22 ( 3221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 320 time to evaluate : 0.987 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: G 35 PHE cc_start: 0.7759 (m-80) cc_final: 0.7476 (m-80) REVERT: G 137 ASN cc_start: 0.8780 (t0) cc_final: 0.8168 (t0) REVERT: G 142 MET cc_start: 0.8443 (mtt) cc_final: 0.8150 (mtt) REVERT: H 185 TYR cc_start: 0.8884 (p90) cc_final: 0.8597 (p90) REVERT: I 116 ASP cc_start: 0.6332 (p0) cc_final: 0.6001 (t70) REVERT: I 142 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7608 (mt-10) REVERT: I 213 LEU cc_start: 0.8667 (mt) cc_final: 0.8234 (mt) REVERT: I 369 MET cc_start: 0.8118 (tmm) cc_final: 0.7867 (tmm) REVERT: I 422 LYS cc_start: 0.7248 (mptt) cc_final: 0.5953 (mptt) REVERT: I 516 ASP cc_start: 0.7091 (p0) cc_final: 0.6487 (p0) REVERT: I 788 SER cc_start: 0.9156 (m) cc_final: 0.8738 (p) REVERT: I 798 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7121 (mm-40) REVERT: I 1085 MET cc_start: 0.9033 (mmm) cc_final: 0.8638 (mmm) REVERT: I 1273 MET cc_start: 0.8422 (mtp) cc_final: 0.8034 (mtt) REVERT: J 96 LYS cc_start: 0.8323 (ttmt) cc_final: 0.7952 (mtpt) REVERT: J 97 VAL cc_start: 0.7639 (t) cc_final: 0.7276 (t) REVERT: J 100 GLU cc_start: 0.8171 (mp0) cc_final: 0.7641 (mp0) REVERT: J 137 ARG cc_start: 0.8554 (mtp-110) cc_final: 0.8141 (ptp90) REVERT: J 301 GLU cc_start: 0.8625 (tp30) cc_final: 0.8341 (tm-30) REVERT: J 356 THR cc_start: 0.8663 (m) cc_final: 0.8449 (m) REVERT: J 398 LYS cc_start: 0.8243 (mttt) cc_final: 0.7865 (mtmm) REVERT: J 504 GLN cc_start: 0.7689 (mp10) cc_final: 0.7274 (mp10) REVERT: J 799 ARG cc_start: 0.8939 (mtm110) cc_final: 0.8237 (mtm110) REVERT: J 1123 ARG cc_start: 0.8249 (mtt180) cc_final: 0.8016 (mmm160) REVERT: J 1254 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7904 (mt-10) REVERT: K 43 ASN cc_start: 0.9031 (t0) cc_final: 0.8702 (t0) outliers start: 86 outliers final: 57 residues processed: 375 average time/residue: 0.1653 time to fit residues: 102.0039 Evaluate side-chains 352 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 295 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 692 THR Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 302 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 153 optimal weight: 0.3980 chunk 133 optimal weight: 7.9990 chunk 282 optimal weight: 40.0000 chunk 105 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 204 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1061 GLN ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 HIS J 495 ASN ** J 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.107939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.080050 restraints weight = 71442.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.082404 restraints weight = 37265.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.083973 restraints weight = 24490.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.084945 restraints weight = 18865.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.085409 restraints weight = 16202.116| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27432 Z= 0.187 Angle : 0.682 13.666 37487 Z= 0.339 Chirality : 0.049 0.455 4317 Planarity : 0.004 0.078 4558 Dihedral : 15.022 174.105 4562 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.59 % Allowed : 17.66 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3152 helix: 1.42 (0.15), residues: 1136 sheet: 0.51 (0.25), residues: 409 loop : -0.13 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 133 TYR 0.047 0.002 TYR J 723 PHE 0.032 0.002 PHE I1025 TRP 0.008 0.001 TRP I1276 HIS 0.023 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (27432) covalent geometry : angle 0.68205 / 0.34 (37487) hydrogen bonds : bond 0.04247 / 4.73 ( 1140) hydrogen bonds : angle 5.01657 / 5.15 ( 3221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 314 time to evaluate : 0.945 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: G 35 PHE cc_start: 0.7817 (m-80) cc_final: 0.7549 (m-80) REVERT: G 137 ASN cc_start: 0.8789 (t0) cc_final: 0.8320 (t0) REVERT: G 142 MET cc_start: 0.8392 (mtt) cc_final: 0.8170 (mtt) REVERT: G 185 TYR cc_start: 0.8775 (p90) cc_final: 0.8550 (p90) REVERT: H 185 TYR cc_start: 0.8936 (p90) cc_final: 0.8640 (p90) REVERT: I 116 ASP cc_start: 0.6342 (p0) cc_final: 0.6003 (t70) REVERT: I 142 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7597 (mt-10) REVERT: I 422 LYS cc_start: 0.7300 (mptt) cc_final: 0.6961 (mptt) REVERT: I 516 ASP cc_start: 0.7083 (p0) cc_final: 0.6431 (p0) REVERT: I 788 SER cc_start: 0.9148 (m) cc_final: 0.8751 (p) REVERT: I 798 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7164 (mm-40) REVERT: I 1085 MET cc_start: 0.9055 (mmm) cc_final: 0.8593 (mmm) REVERT: I 1244 HIS cc_start: 0.6740 (OUTLIER) cc_final: 0.5670 (t70) REVERT: I 1273 MET cc_start: 0.8395 (mtp) cc_final: 0.7991 (mtt) REVERT: J 96 LYS cc_start: 0.8324 (ttmt) cc_final: 0.7960 (mtpt) REVERT: J 97 VAL cc_start: 0.7502 (t) cc_final: 0.7221 (t) REVERT: J 100 GLU cc_start: 0.8185 (mp0) cc_final: 0.7691 (mp0) REVERT: J 137 ARG cc_start: 0.8553 (mtp-110) cc_final: 0.8134 (ptp90) REVERT: J 352 ARG cc_start: 0.7780 (ttm-80) cc_final: 0.7370 (ttm-80) REVERT: J 504 GLN cc_start: 0.7694 (mp10) cc_final: 0.7232 (mp10) REVERT: J 1123 ARG cc_start: 0.8248 (mtt180) cc_final: 0.8030 (mtp180) REVERT: J 1155 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8626 (mp) REVERT: J 1189 MET cc_start: 0.7858 (mmt) cc_final: 0.7377 (tpt) REVERT: J 1254 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7863 (mt-10) REVERT: K 43 ASN cc_start: 0.9022 (t0) cc_final: 0.8721 (t0) outliers start: 97 outliers final: 67 residues processed: 380 average time/residue: 0.1703 time to fit residues: 106.0633 Evaluate side-chains 357 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 288 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 692 THR Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1347 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 57 optimal weight: 20.0000 chunk 219 optimal weight: 0.7980 chunk 280 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 229 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 304 optimal weight: 9.9990 chunk 316 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 234 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 150 HIS I 165 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.109073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.080991 restraints weight = 71986.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.083394 restraints weight = 37579.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.084977 restraints weight = 24753.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.085962 restraints weight = 19104.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.086501 restraints weight = 16400.024| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27432 Z= 0.138 Angle : 0.662 14.306 37487 Z= 0.327 Chirality : 0.048 0.345 4317 Planarity : 0.004 0.052 4558 Dihedral : 15.008 173.487 4562 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.92 % Allowed : 19.36 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.14), residues: 3152 helix: 1.40 (0.15), residues: 1137 sheet: 0.48 (0.25), residues: 408 loop : -0.16 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 52 TYR 0.038 0.002 TYR J 723 PHE 0.028 0.001 PHE I1025 TRP 0.013 0.001 TRP J 580 HIS 0.006 0.001 HIS I1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (27432) covalent geometry : angle 0.66160 / 0.33 (37487) hydrogen bonds : bond 0.04099 / 4.58 ( 1140) hydrogen bonds : angle 4.89749 / 5.02 ( 3221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 336 time to evaluate : 1.063 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: G 35 PHE cc_start: 0.7863 (m-80) cc_final: 0.7605 (m-80) REVERT: G 137 ASN cc_start: 0.8762 (t0) cc_final: 0.8287 (t0) REVERT: G 185 TYR cc_start: 0.8761 (p90) cc_final: 0.8487 (p90) REVERT: H 104 LYS cc_start: 0.7285 (mmmt) cc_final: 0.6830 (tttt) REVERT: H 185 TYR cc_start: 0.8903 (p90) cc_final: 0.8625 (p90) REVERT: I 116 ASP cc_start: 0.6275 (p0) cc_final: 0.6014 (t70) REVERT: I 142 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7681 (mt-10) REVERT: I 427 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8132 (m-30) REVERT: I 516 ASP cc_start: 0.7084 (p0) cc_final: 0.6477 (p0) REVERT: I 788 SER cc_start: 0.9083 (m) cc_final: 0.8677 (p) REVERT: I 798 GLN cc_start: 0.7543 (mm-40) cc_final: 0.7046 (mm-40) REVERT: I 1085 MET cc_start: 0.9004 (mmm) cc_final: 0.8563 (mmm) REVERT: I 1244 HIS cc_start: 0.6667 (OUTLIER) cc_final: 0.5517 (t70) REVERT: I 1273 MET cc_start: 0.8352 (mtp) cc_final: 0.8112 (mtp) REVERT: J 96 LYS cc_start: 0.8322 (ttmt) cc_final: 0.8027 (mttt) REVERT: J 100 GLU cc_start: 0.8211 (mp0) cc_final: 0.7713 (mp0) REVERT: J 137 ARG cc_start: 0.8517 (mtp-110) cc_final: 0.8128 (ptp90) REVERT: J 330 MET cc_start: 0.7725 (mtm) cc_final: 0.7518 (ptm) REVERT: J 375 GLU cc_start: 0.7778 (mp0) cc_final: 0.7361 (mp0) REVERT: J 504 GLN cc_start: 0.7639 (mp10) cc_final: 0.7187 (mp10) REVERT: J 642 ASP cc_start: 0.8243 (m-30) cc_final: 0.7976 (m-30) REVERT: J 1123 ARG cc_start: 0.8255 (mtt180) cc_final: 0.7991 (mtp-110) REVERT: J 1189 MET cc_start: 0.7776 (mmt) cc_final: 0.7273 (tpt) REVERT: J 1254 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7831 (mt-10) REVERT: K 43 ASN cc_start: 0.9046 (t0) cc_final: 0.8843 (t0) outliers start: 79 outliers final: 61 residues processed: 387 average time/residue: 0.1744 time to fit residues: 109.6131 Evaluate side-chains 355 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 292 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 4 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 chunk 150 optimal weight: 0.0670 chunk 217 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 110 optimal weight: 0.2980 chunk 234 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 450 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.109425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.082035 restraints weight = 71374.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.084389 restraints weight = 37366.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.085942 restraints weight = 24575.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.086905 restraints weight = 18946.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.087483 restraints weight = 16268.596| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27432 Z= 0.132 Angle : 0.656 14.273 37487 Z= 0.324 Chirality : 0.048 0.342 4317 Planarity : 0.004 0.051 4558 Dihedral : 14.981 173.085 4562 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.22 % Allowed : 19.59 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.14), residues: 3152 helix: 1.42 (0.15), residues: 1137 sheet: 0.50 (0.25), residues: 408 loop : -0.19 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J1372 TYR 0.027 0.001 TYR H 177 PHE 0.026 0.001 PHE I1025 TRP 0.009 0.001 TRP J 580 HIS 0.006 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (27432) covalent geometry : angle 0.65598 / 0.32 (37487) hydrogen bonds : bond 0.03999 / 4.48 ( 1140) hydrogen bonds : angle 4.81827 / 4.95 ( 3221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 313 time to evaluate : 1.215 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: G 35 PHE cc_start: 0.7799 (m-80) cc_final: 0.7562 (m-80) REVERT: G 137 ASN cc_start: 0.8700 (t0) cc_final: 0.8313 (t0) REVERT: G 185 TYR cc_start: 0.8740 (p90) cc_final: 0.8464 (p90) REVERT: H 185 TYR cc_start: 0.8861 (p90) cc_final: 0.8578 (p90) REVERT: I 116 ASP cc_start: 0.6191 (p0) cc_final: 0.5934 (t70) REVERT: I 142 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7637 (mt-10) REVERT: I 427 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.8083 (m-30) REVERT: I 516 ASP cc_start: 0.7034 (p0) cc_final: 0.6463 (p0) REVERT: I 788 SER cc_start: 0.9075 (m) cc_final: 0.8662 (p) REVERT: I 798 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7236 (mm-40) REVERT: I 1085 MET cc_start: 0.9017 (mmm) cc_final: 0.8560 (mmm) REVERT: I 1244 HIS cc_start: 0.6765 (OUTLIER) cc_final: 0.5601 (t70) REVERT: I 1273 MET cc_start: 0.8308 (mtp) cc_final: 0.8069 (mtp) REVERT: J 96 LYS cc_start: 0.8279 (ttmt) cc_final: 0.8022 (mtpt) REVERT: J 100 GLU cc_start: 0.8141 (mp0) cc_final: 0.7709 (mp0) REVERT: J 137 ARG cc_start: 0.8460 (mtp-110) cc_final: 0.8119 (ptp90) REVERT: J 352 ARG cc_start: 0.7754 (ttm-80) cc_final: 0.7469 (ttm-80) REVERT: J 375 GLU cc_start: 0.7749 (mp0) cc_final: 0.7315 (mp0) REVERT: J 504 GLN cc_start: 0.7661 (mp10) cc_final: 0.7195 (mp10) REVERT: J 642 ASP cc_start: 0.8139 (m-30) cc_final: 0.7880 (m-30) REVERT: J 821 MET cc_start: 0.8860 (tpp) cc_final: 0.8660 (tpp) REVERT: J 1123 ARG cc_start: 0.8217 (mtt180) cc_final: 0.7991 (mtp-110) REVERT: J 1189 MET cc_start: 0.7734 (mmt) cc_final: 0.7205 (tpt) REVERT: J 1254 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7827 (mt-10) REVERT: J 1370 MET cc_start: 0.7617 (mmp) cc_final: 0.7080 (mmt) outliers start: 87 outliers final: 67 residues processed: 373 average time/residue: 0.1755 time to fit residues: 107.0200 Evaluate side-chains 366 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 297 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 270 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 295 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 292 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 1 optimal weight: 30.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 450 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 477 GLN ** J 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.107124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.079293 restraints weight = 71908.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.081643 restraints weight = 37613.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.083192 restraints weight = 24718.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.084168 restraints weight = 19047.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.084602 restraints weight = 16304.062| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27432 Z= 0.218 Angle : 0.690 14.364 37487 Z= 0.344 Chirality : 0.048 0.343 4317 Planarity : 0.004 0.065 4558 Dihedral : 15.024 172.749 4562 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.33 % Allowed : 20.29 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3152 helix: 1.34 (0.15), residues: 1144 sheet: 0.45 (0.26), residues: 376 loop : -0.20 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J1330 TYR 0.030 0.002 TYR I1229 PHE 0.036 0.002 PHE I1025 TRP 0.009 0.001 TRP J 580 HIS 0.007 0.001 HIS I 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 (27432) covalent geometry : angle 0.69037 / 0.34 (37487) hydrogen bonds : bond 0.04186 / 4.66 ( 1140) hydrogen bonds : angle 4.88045 / 5.02 ( 3221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 287 time to evaluate : 0.980 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: G 35 PHE cc_start: 0.7868 (m-80) cc_final: 0.7663 (m-80) REVERT: H 104 LYS cc_start: 0.7255 (mmmt) cc_final: 0.6899 (tttt) REVERT: H 185 TYR cc_start: 0.8963 (p90) cc_final: 0.8604 (p90) REVERT: I 116 ASP cc_start: 0.6458 (p0) cc_final: 0.6146 (t70) REVERT: I 142 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7814 (mt-10) REVERT: I 427 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8143 (m-30) REVERT: I 516 ASP cc_start: 0.7092 (p0) cc_final: 0.6499 (p0) REVERT: I 788 SER cc_start: 0.9152 (m) cc_final: 0.8857 (p) REVERT: I 798 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7344 (mm-40) REVERT: I 862 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9143 (mm) REVERT: I 1085 MET cc_start: 0.9097 (mmm) cc_final: 0.8567 (mmm) REVERT: I 1119 MET cc_start: 0.8594 (tpp) cc_final: 0.8352 (tpp) REVERT: I 1244 HIS cc_start: 0.6937 (OUTLIER) cc_final: 0.5780 (t70) REVERT: J 96 LYS cc_start: 0.8363 (ttmt) cc_final: 0.8038 (mtpt) REVERT: J 100 GLU cc_start: 0.8178 (mp0) cc_final: 0.7741 (mp0) REVERT: J 137 ARG cc_start: 0.8474 (mtp-110) cc_final: 0.8116 (ptp90) REVERT: J 140 TYR cc_start: 0.8173 (m-10) cc_final: 0.7887 (m-10) REVERT: J 504 GLN cc_start: 0.7776 (mp10) cc_final: 0.7335 (mp10) REVERT: J 799 ARG cc_start: 0.8927 (mtm110) cc_final: 0.8048 (mtm110) REVERT: J 1123 ARG cc_start: 0.8302 (mtt180) cc_final: 0.8029 (mtp-110) REVERT: J 1155 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8678 (mp) REVERT: J 1254 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7967 (mt-10) outliers start: 90 outliers final: 72 residues processed: 352 average time/residue: 0.1730 time to fit residues: 99.4700 Evaluate side-chains 357 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 281 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 117 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 136 optimal weight: 0.0050 chunk 52 optimal weight: 10.0000 chunk 273 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 296 optimal weight: 0.0670 chunk 95 optimal weight: 0.0270 chunk 133 optimal weight: 0.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 450 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 ASN ** J 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.110499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.083050 restraints weight = 71865.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.085556 restraints weight = 36558.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.087190 restraints weight = 23613.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.088212 restraints weight = 18038.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.088825 restraints weight = 15403.181| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27432 Z= 0.126 Angle : 0.666 14.359 37487 Z= 0.328 Chirality : 0.047 0.333 4317 Planarity : 0.004 0.057 4558 Dihedral : 15.013 172.256 4562 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.74 % Allowed : 21.03 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.15), residues: 3152 helix: 1.32 (0.15), residues: 1137 sheet: 0.40 (0.26), residues: 381 loop : -0.20 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 52 TYR 0.031 0.001 TYR I1229 PHE 0.037 0.001 PHE I1025 TRP 0.014 0.002 TRP J 580 HIS 0.006 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (27432) covalent geometry : angle 0.66557 / 0.33 (37487) hydrogen bonds : bond 0.03955 / 4.44 ( 1140) hydrogen bonds : angle 4.76747 / 4.90 ( 3221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 323 time to evaluate : 1.021 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: G 35 PHE cc_start: 0.7828 (m-80) cc_final: 0.7611 (m-80) REVERT: G 137 ASN cc_start: 0.8728 (t0) cc_final: 0.8383 (t0) REVERT: H 104 LYS cc_start: 0.7095 (mmmt) cc_final: 0.6832 (tttt) REVERT: H 185 TYR cc_start: 0.8903 (p90) cc_final: 0.8587 (p90) REVERT: I 47 TYR cc_start: 0.4748 (m-80) cc_final: 0.4459 (m-10) REVERT: I 116 ASP cc_start: 0.6165 (p0) cc_final: 0.5922 (t70) REVERT: I 142 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7723 (mt-10) REVERT: I 516 ASP cc_start: 0.7089 (p0) cc_final: 0.6517 (p0) REVERT: I 788 SER cc_start: 0.9031 (m) cc_final: 0.8691 (p) REVERT: I 798 GLN cc_start: 0.7393 (mm-40) cc_final: 0.7080 (mm-40) REVERT: I 862 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9109 (mm) REVERT: I 1085 MET cc_start: 0.9027 (mmm) cc_final: 0.8531 (mmm) REVERT: I 1244 HIS cc_start: 0.6785 (OUTLIER) cc_final: 0.5712 (t70) REVERT: I 1276 TRP cc_start: 0.8392 (m-10) cc_final: 0.8065 (m-10) REVERT: J 96 LYS cc_start: 0.8338 (ttmt) cc_final: 0.8004 (mtmt) REVERT: J 100 GLU cc_start: 0.8131 (mp0) cc_final: 0.7646 (mp0) REVERT: J 137 ARG cc_start: 0.8356 (mtp-110) cc_final: 0.8151 (ptp90) REVERT: J 330 MET cc_start: 0.7959 (ptm) cc_final: 0.7631 (ptm) REVERT: J 375 GLU cc_start: 0.7789 (mp0) cc_final: 0.7451 (mp0) REVERT: J 382 TYR cc_start: 0.9089 (m-80) cc_final: 0.8862 (m-80) REVERT: J 504 GLN cc_start: 0.7670 (mp10) cc_final: 0.7210 (mp10) REVERT: J 642 ASP cc_start: 0.8106 (m-30) cc_final: 0.7872 (m-30) REVERT: J 1123 ARG cc_start: 0.8271 (mtt180) cc_final: 0.8017 (mtp-110) REVERT: J 1155 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8642 (mp) REVERT: J 1254 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7826 (mt-10) REVERT: J 1370 MET cc_start: 0.7777 (mmp) cc_final: 0.7238 (mmt) REVERT: K 69 ARG cc_start: 0.8314 (mtp-110) cc_final: 0.7972 (ttm110) REVERT: K 74 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7347 (tp30) outliers start: 74 outliers final: 57 residues processed: 372 average time/residue: 0.1719 time to fit residues: 104.4951 Evaluate side-chains 363 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 302 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 62 GLN Chi-restraints excluded: chain K residue 74 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 281 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 291 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 292 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 41 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.105293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.077519 restraints weight = 71912.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.079799 restraints weight = 37820.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.081305 restraints weight = 25009.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.082251 restraints weight = 19329.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.082678 restraints weight = 16612.870| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 27432 Z= 0.281 Angle : 0.749 12.815 37487 Z= 0.374 Chirality : 0.049 0.336 4317 Planarity : 0.005 0.059 4558 Dihedral : 15.103 172.064 4562 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.92 % Allowed : 20.84 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.15), residues: 3152 helix: 1.21 (0.15), residues: 1151 sheet: 0.33 (0.27), residues: 377 loop : -0.26 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I1246 TYR 0.035 0.002 TYR I1229 PHE 0.038 0.002 PHE I1025 TRP 0.011 0.002 TRP I 997 HIS 0.010 0.001 HIS I 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.28 (27432) covalent geometry : angle 0.74888 / 0.37 (37487) hydrogen bonds : bond 0.04427 / 4.94 ( 1140) hydrogen bonds : angle 4.95817 / 5.12 ( 3221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 292 time to evaluate : 1.024 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: G 35 PHE cc_start: 0.7965 (m-80) cc_final: 0.7741 (m-80) REVERT: G 137 ASN cc_start: 0.8839 (t0) cc_final: 0.8524 (t0) REVERT: H 185 TYR cc_start: 0.9062 (p90) cc_final: 0.8690 (p90) REVERT: I 116 ASP cc_start: 0.6350 (p0) cc_final: 0.6037 (t70) REVERT: I 213 LEU cc_start: 0.8961 (mt) cc_final: 0.8760 (mt) REVERT: I 516 ASP cc_start: 0.7155 (p0) cc_final: 0.6538 (p0) REVERT: I 788 SER cc_start: 0.9225 (m) cc_final: 0.9003 (p) REVERT: I 798 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7240 (mm-40) REVERT: I 862 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9157 (mm) REVERT: I 1085 MET cc_start: 0.9109 (mmm) cc_final: 0.8654 (mmm) REVERT: I 1244 HIS cc_start: 0.7096 (OUTLIER) cc_final: 0.5890 (t70) REVERT: J 96 LYS cc_start: 0.8433 (ttmt) cc_final: 0.8087 (mtmt) REVERT: J 100 GLU cc_start: 0.8104 (mp0) cc_final: 0.7657 (mp0) REVERT: J 137 ARG cc_start: 0.8441 (mtp-110) cc_final: 0.8166 (ptp90) REVERT: J 330 MET cc_start: 0.7897 (ptm) cc_final: 0.7581 (ptm) REVERT: J 375 GLU cc_start: 0.7806 (mp0) cc_final: 0.7404 (mp0) REVERT: J 417 ARG cc_start: 0.8092 (ptp-110) cc_final: 0.7843 (ptm-80) REVERT: J 504 GLN cc_start: 0.7862 (mp10) cc_final: 0.7439 (mp10) REVERT: J 698 MET cc_start: 0.9428 (mmm) cc_final: 0.9012 (tpp) REVERT: J 821 MET cc_start: 0.8872 (tpp) cc_final: 0.8592 (tpp) REVERT: J 1123 ARG cc_start: 0.8252 (mtt180) cc_final: 0.7996 (mtp-110) REVERT: J 1155 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8707 (mp) REVERT: J 1254 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8056 (mt-10) REVERT: J 1370 MET cc_start: 0.7868 (mmp) cc_final: 0.7158 (mmt) outliers start: 79 outliers final: 71 residues processed: 347 average time/residue: 0.1619 time to fit residues: 92.9851 Evaluate side-chains 355 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 281 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 286 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 273 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 271 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.107578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.080324 restraints weight = 70876.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.082658 restraints weight = 36666.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.084183 restraints weight = 24030.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.085150 restraints weight = 18477.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.085676 restraints weight = 15806.018| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27432 Z= 0.152 Angle : 0.679 13.633 37487 Z= 0.338 Chirality : 0.047 0.328 4317 Planarity : 0.004 0.064 4558 Dihedral : 15.101 171.554 4562 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.59 % Allowed : 21.25 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.15), residues: 3152 helix: 1.24 (0.15), residues: 1148 sheet: 0.38 (0.27), residues: 376 loop : -0.24 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 69 TYR 0.036 0.002 TYR I1229 PHE 0.036 0.002 PHE I1025 TRP 0.012 0.002 TRP J 580 HIS 0.005 0.001 HIS I1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (27432) covalent geometry : angle 0.67880 / 0.34 (37487) hydrogen bonds : bond 0.04042 / 4.53 ( 1140) hydrogen bonds : angle 4.81086 / 4.97 ( 3221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4984.49 seconds wall clock time: 87 minutes 6.18 seconds (5226.18 seconds total)