Starting phenix.real_space_refine on Sun Jul 5 09:45:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g2w_29683/07_2026/8g2w_29683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g2w_29683/07_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_29683/07_2026/8g2w_29683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g2w_29683/07_2026/8g2w_29683.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8g2w_29683/07_2026/8g2w_29683.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g2w_29683/07_2026/8g2w_29683.cif" model { file = "/net/cci-nas-00/data/ceres_data/8g2w_29683/07_2026/8g2w_29683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g2w_29683/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNA': 47} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 11, 'rna3p': 35} 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: 4.59, per 1000 atoms: 0.17 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: 2.13 Conformation dependent library (CDL) restraints added in 878.1 milliseconds 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 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: 3.03 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: 6.20 Time building geometry restraints manager: 2.73 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 1.50e-02 4.44e+03 1.63e+01 bond pdb=" O3' DC B 17 " pdb=" P DG B 18 " ideal model delta sigma weight residual 1.607 1.664 -0.057 1.50e-02 4.44e+03 1.47e+01 bond pdb=" N GLN I1257 " pdb=" CA GLN I1257 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.04e-02 9.25e+03 1.27e+01 ... (remaining 27427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 36879 2.16 - 4.31: 547 4.31 - 6.47: 50 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: 16062 35.88 - 71.76: 513 71.76 - 107.64: 39 107.64 - 143.52: 5 143.52 - 179.40: 2 Dihedral angle restraints: 16621 sinusoidal: 7518 harmonic: 9103 Sorted by residual: dihedral pdb=" O4' U R 15 " pdb=" C1' U R 15 " pdb=" N1 U R 15 " pdb=" C2 U R 15 " ideal model delta sinusoidal sigma weight residual 200.00 59.10 140.90 1 1.50e+01 4.44e-03 7.58e+01 dihedral pdb=" O4' C R 17 " pdb=" C1' C R 17 " pdb=" N1 C R 17 " pdb=" C2 C R 17 " ideal model delta sinusoidal sigma weight residual 200.00 64.11 135.89 1 1.50e+01 4.44e-03 7.33e+01 dihedral pdb=" CA PHE I 57 " pdb=" C PHE I 57 " pdb=" N PRO I 58 " pdb=" CA PRO I 58 " ideal model delta harmonic sigma weight residual 180.00 157.80 22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 16618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3789 0.066 - 0.132: 490 0.132 - 0.198: 30 0.198 - 0.265: 6 0.265 - 0.331: 2 Chirality restraints: 4317 Sorted by residual: chirality pdb=" C3' DG B 22 " pdb=" C4' DG B 22 " pdb=" O3' DG B 22 " pdb=" C2' DG B 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.40 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA GLN I1257 " pdb=" N GLN I1257 " pdb=" C GLN I1257 " pdb=" CB GLN I1257 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 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 2.41 -2.64 -0.23 2.00e-01 2.50e+01 1.37e+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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 24.220 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.450 ------------------------------------------------------------------------------- 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= 0.224 Angle : 0.635 10.780 37487 Z= 0.389 Chirality : 0.043 0.331 4317 Planarity : 0.004 0.055 4558 Dihedral : 16.756 179.396 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 0.00371 / 0.22 (27432) covalent geometry : angle 0.63476 / 0.39 (37487) hydrogen bonds : bond 0.17679 / 19.32 ( 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 : 0.969 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: 0.1856 time to fit residues: 198.5057 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 : 1.002 ------------------------------------------------------------------------------- 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 J1235 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.116938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.089613 restraints weight = 72780.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.092421 restraints weight = 32954.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.094230 restraints weight = 20123.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.095357 restraints weight = 14967.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.096024 restraints weight = 12624.205| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 27432 Z= 0.210 Angle : 0.689 13.306 37487 Z= 0.361 Chirality : 0.045 0.362 4317 Planarity : 0.005 0.059 4558 Dihedral : 14.424 173.907 4562 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.22 % Allowed : 13.33 % Favored : 84.45 % 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: 1.05 (0.14), residues: 3152 helix: 1.48 (0.15), residues: 1141 sheet: 0.91 (0.25), residues: 423 loop : 0.14 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG J 978 TYR 0.031 0.002 TYR I1229 PHE 0.017 0.002 PHE J 377 TRP 0.013 0.002 TRP J 580 HIS 0.011 0.002 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (27432) covalent geometry : angle 0.68947 / 0.36 (37487) hydrogen bonds : bond 0.05136 / 5.67 ( 1140) hydrogen bonds : angle 5.60731 / 5.66 ( 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 446 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 386 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 156 SER cc_start: 0.9406 (p) cc_final: 0.9117 (t) REVERT: H 29 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6846 (mm-30) REVERT: H 32 GLU cc_start: 0.7358 (tp30) cc_final: 0.7009 (mm-30) REVERT: H 131 CYS cc_start: 0.7051 (p) cc_final: 0.6414 (p) REVERT: H 185 TYR cc_start: 0.8896 (p90) cc_final: 0.8594 (p90) REVERT: I 116 ASP cc_start: 0.6662 (p0) cc_final: 0.6298 (t70) REVERT: I 142 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7685 (mt-10) REVERT: I 414 ILE cc_start: 0.9178 (mm) cc_final: 0.8630 (tp) REVERT: I 515 MET cc_start: 0.8321 (tpt) cc_final: 0.8111 (tpp) REVERT: I 516 ASP cc_start: 0.7410 (p0) cc_final: 0.6629 (p0) REVERT: I 788 SER cc_start: 0.9169 (m) cc_final: 0.8803 (p) REVERT: I 798 GLN cc_start: 0.7753 (mm-40) cc_final: 0.6974 (mm-40) REVERT: I 811 ASN cc_start: 0.9261 (OUTLIER) cc_final: 0.9021 (p0) REVERT: I 1085 MET cc_start: 0.9148 (mmm) cc_final: 0.8720 (mmm) REVERT: I 1117 LEU cc_start: 0.9463 (tp) cc_final: 0.9253 (tp) REVERT: I 1273 MET cc_start: 0.8469 (mtp) cc_final: 0.8021 (mtt) REVERT: J 96 LYS cc_start: 0.8155 (ttmt) cc_final: 0.7858 (mtpt) REVERT: J 97 VAL cc_start: 0.7582 (t) cc_final: 0.6966 (t) REVERT: J 100 GLU cc_start: 0.8221 (mp0) cc_final: 0.7599 (mp0) REVERT: J 137 ARG cc_start: 0.8476 (mtp-110) cc_final: 0.7959 (ptp90) REVERT: J 199 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8184 (pm20) REVERT: J 301 GLU cc_start: 0.8598 (tp30) cc_final: 0.8234 (tm-30) REVERT: J 418 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7124 (mm-30) REVERT: J 445 LYS cc_start: 0.8605 (mttt) cc_final: 0.8346 (mttt) REVERT: J 466 MET cc_start: 0.8176 (mtm) cc_final: 0.7948 (mtt) REVERT: J 479 GLU cc_start: 0.8454 (tt0) cc_final: 0.8250 (tp30) REVERT: J 504 GLN cc_start: 0.7727 (mp10) cc_final: 0.7323 (mp10) REVERT: J 532 GLU cc_start: 0.8192 (tt0) cc_final: 0.7986 (tt0) REVERT: J 656 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7616 (mt-10) REVERT: J 723 TYR cc_start: 0.8872 (t80) cc_final: 0.8640 (t80) REVERT: J 835 LEU cc_start: 0.8347 (tp) cc_final: 0.8090 (tp) REVERT: J 1123 ARG cc_start: 0.8267 (mtt180) cc_final: 0.7938 (mtp-110) REVERT: J 1250 ASP cc_start: 0.8611 (m-30) cc_final: 0.8372 (m-30) REVERT: J 1254 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8043 (mt-10) REVERT: K 43 ASN cc_start: 0.8961 (t0) cc_final: 0.8559 (t0) outliers start: 60 outliers final: 36 residues processed: 424 average time/residue: 0.1611 time to fit residues: 109.4399 Evaluate side-chains 349 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 311 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 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 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 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 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: 6.9990 chunk 301 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 222 optimal weight: 0.1980 chunk 62 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 490 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 628 HIS ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1209 GLN I1244 HIS ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 435 GLN ** 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 = 0.3730 r_free = 0.3730 target = 0.107533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.079976 restraints weight = 71313.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.082363 restraints weight = 36967.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.083936 restraints weight = 24069.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.084935 restraints weight = 18451.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.085498 restraints weight = 15719.282| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27432 Z= 0.220 Angle : 0.651 12.747 37487 Z= 0.341 Chirality : 0.043 0.212 4317 Planarity : 0.004 0.055 4558 Dihedral : 14.428 174.945 4562 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.07 % Allowed : 15.81 % Favored : 81.12 % 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: 1.43 (0.15), residues: 1132 sheet: 0.67 (0.26), residues: 407 loop : -0.01 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 978 TYR 0.034 0.002 TYR H 177 PHE 0.021 0.002 PHE I1025 TRP 0.015 0.002 TRP I1276 HIS 0.013 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.22 (27432) covalent geometry : angle 0.65106 / 0.34 (37487) hydrogen bonds : bond 0.04717 / 5.20 ( 1140) hydrogen bonds : angle 5.31401 / 5.42 ( 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 430 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 347 time to evaluate : 1.032 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: 0.7806 (m-80) cc_final: 0.7481 (m-80) REVERT: G 137 ASN cc_start: 0.8817 (t0) cc_final: 0.8209 (t0) REVERT: G 185 TYR cc_start: 0.8838 (p90) cc_final: 0.8633 (p90) REVERT: H 185 TYR cc_start: 0.8918 (p90) cc_final: 0.8604 (p90) REVERT: I 116 ASP cc_start: 0.6351 (p0) cc_final: 0.5966 (t70) REVERT: I 142 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7617 (mt-10) REVERT: I 193 ASN cc_start: 0.8044 (m-40) cc_final: 0.7762 (t0) REVERT: I 422 LYS cc_start: 0.7221 (mptt) cc_final: 0.6783 (mptt) REVERT: I 516 ASP cc_start: 0.7221 (p0) cc_final: 0.6448 (p0) REVERT: I 785 ASP cc_start: 0.6595 (m-30) cc_final: 0.6386 (p0) REVERT: I 788 SER cc_start: 0.9145 (m) cc_final: 0.8750 (p) REVERT: I 798 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7243 (mm-40) REVERT: I 1085 MET cc_start: 0.9053 (mmm) cc_final: 0.8603 (mmm) REVERT: I 1273 MET cc_start: 0.8419 (mtp) cc_final: 0.8032 (mtt) REVERT: J 96 LYS cc_start: 0.8351 (ttmt) cc_final: 0.8007 (mtpt) REVERT: J 97 VAL cc_start: 0.7723 (t) cc_final: 0.7080 (t) REVERT: J 100 GLU cc_start: 0.8150 (mp0) cc_final: 0.7646 (mp0) REVERT: J 137 ARG cc_start: 0.8452 (mtp-110) cc_final: 0.8118 (ptp90) REVERT: J 301 GLU cc_start: 0.8657 (tp30) cc_final: 0.8251 (tm-30) REVERT: J 330 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7402 (ptm) REVERT: J 504 GLN cc_start: 0.7736 (mp10) cc_final: 0.7363 (mp10) REVERT: J 532 GLU cc_start: 0.8130 (tt0) cc_final: 0.7922 (tt0) REVERT: J 697 MET cc_start: 0.8198 (ttp) cc_final: 0.7883 (ttp) REVERT: J 1123 ARG cc_start: 0.8201 (mtt180) cc_final: 0.7919 (mtp-110) REVERT: J 1250 ASP cc_start: 0.8459 (m-30) cc_final: 0.8247 (m-30) REVERT: J 1254 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7922 (mt-10) REVERT: K 11 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8221 (mp0) REVERT: K 43 ASN cc_start: 0.8986 (t0) cc_final: 0.8688 (t0) outliers start: 83 outliers final: 53 residues processed: 400 average time/residue: 0.1677 time to fit residues: 106.9164 Evaluate side-chains 356 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 301 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 71 VAL Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 681 MET 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 939 VAL Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1077 SER 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 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 245 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 330 MET 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 618 VAL 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 1351 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 11 GLU 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: 0.9990 chunk 36 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 202 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 HIS I 165 HIS I 450 ASN I 490 GLN ** 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** I1209 GLN I1244 HIS ** 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** ** 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 = 0.3763 r_free = 0.3763 target = 0.109392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.081503 restraints weight = 71190.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.083944 restraints weight = 37056.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.085544 restraints weight = 24286.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.086550 restraints weight = 18702.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.087019 restraints weight = 16006.104| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2809 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= 0.135 Angle : 0.612 13.428 37487 Z= 0.317 Chirality : 0.042 0.213 4317 Planarity : 0.004 0.054 4558 Dihedral : 14.396 174.002 4562 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.15 % Allowed : 17.51 % Favored : 79.34 % 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: 0.77 (0.14), residues: 3152 helix: 1.39 (0.15), residues: 1140 sheet: 0.65 (0.26), residues: 395 loop : -0.09 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 220 TYR 0.030 0.002 TYR H 177 PHE 0.030 0.001 PHE I1025 TRP 0.013 0.002 TRP J 580 HIS 0.015 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (27432) covalent geometry : angle 0.61189 / 0.32 (37487) hydrogen bonds : bond 0.04244 / 4.69 ( 1140) hydrogen bonds : angle 5.07806 / 5.19 ( 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 442 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 357 time to evaluate : 0.852 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: 0.7773 (m-80) cc_final: 0.7503 (m-80) REVERT: G 137 ASN cc_start: 0.8760 (t0) cc_final: 0.8268 (t0) REVERT: G 185 TYR cc_start: 0.8760 (p90) cc_final: 0.8503 (p90) REVERT: H 185 TYR cc_start: 0.8884 (p90) cc_final: 0.8589 (p90) REVERT: I 116 ASP cc_start: 0.6206 (p0) cc_final: 0.5890 (t70) REVERT: I 142 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7666 (mt-10) REVERT: I 516 ASP cc_start: 0.7085 (p0) cc_final: 0.6463 (p0) REVERT: I 788 SER cc_start: 0.9027 (m) cc_final: 0.8615 (p) REVERT: I 798 GLN cc_start: 0.7603 (mm-40) cc_final: 0.7204 (mm-40) REVERT: I 1085 MET cc_start: 0.9024 (mmm) cc_final: 0.8599 (mmm) REVERT: I 1273 MET cc_start: 0.8336 (mtp) cc_final: 0.7941 (mtt) REVERT: J 96 LYS cc_start: 0.8341 (ttmt) cc_final: 0.7951 (mtpt) REVERT: J 97 VAL cc_start: 0.7609 (t) cc_final: 0.7241 (t) REVERT: J 100 GLU cc_start: 0.8122 (mp0) cc_final: 0.7588 (mp0) REVERT: J 137 ARG cc_start: 0.8545 (mtp-110) cc_final: 0.8165 (ptp90) REVERT: J 140 TYR cc_start: 0.7840 (m-10) cc_final: 0.7621 (m-10) REVERT: J 301 GLU cc_start: 0.8602 (tp30) cc_final: 0.8269 (tm-30) REVERT: J 330 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7317 (ptm) REVERT: J 398 LYS cc_start: 0.8264 (mttt) cc_final: 0.7896 (mtmm) REVERT: J 504 GLN cc_start: 0.7635 (mp10) cc_final: 0.7231 (mp10) REVERT: J 532 GLU cc_start: 0.8013 (tt0) cc_final: 0.7800 (tt0) REVERT: J 895 CYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6999 (t) REVERT: J 1123 ARG cc_start: 0.8268 (mtt180) cc_final: 0.8039 (mmm160) REVERT: J 1155 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8578 (mp) REVERT: J 1250 ASP cc_start: 0.8383 (m-30) cc_final: 0.8156 (m-30) REVERT: J 1254 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7825 (mt-10) REVERT: K 11 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8125 (mp0) REVERT: K 43 ASN cc_start: 0.9023 (t0) cc_final: 0.8734 (t0) outliers start: 85 outliers final: 49 residues processed: 414 average time/residue: 0.1583 time to fit residues: 107.1579 Evaluate side-chains 358 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 305 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 170 VAL Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 939 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 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1253 LEU 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 237 MET Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 343 LEU 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 505 ASP 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 895 CYS 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 1351 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 21 LEU 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: 0.4980 chunk 201 optimal weight: 0.0870 chunk 239 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 282 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 766 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS ** 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 = 0.3760 r_free = 0.3760 target = 0.109141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.081231 restraints weight = 71485.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.083642 restraints weight = 37207.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.085246 restraints weight = 24403.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.086231 restraints weight = 18781.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.086728 restraints weight = 16123.821| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27432 Z= 0.138 Angle : 0.607 13.099 37487 Z= 0.315 Chirality : 0.043 0.327 4317 Planarity : 0.004 0.067 4558 Dihedral : 14.381 173.217 4562 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.18 % Allowed : 18.10 % Favored : 78.71 % 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: 0.73 (0.14), residues: 3152 helix: 1.37 (0.15), residues: 1138 sheet: 0.57 (0.25), residues: 399 loop : -0.10 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 133 TYR 0.043 0.002 TYR I1229 PHE 0.023 0.001 PHE I1025 TRP 0.016 0.002 TRP I1276 HIS 0.014 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (27432) covalent geometry : angle 0.60734 / 0.31 (37487) hydrogen bonds : bond 0.04121 / 4.58 ( 1140) hydrogen bonds : angle 4.95079 / 5.09 ( 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 402 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 316 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7829 (m-80) cc_final: 0.7583 (m-80) REVERT: H 177 TYR cc_start: 0.7905 (m-10) cc_final: 0.7693 (m-80) REVERT: H 185 TYR cc_start: 0.8882 (p90) cc_final: 0.8588 (p90) REVERT: I 116 ASP cc_start: 0.6282 (p0) cc_final: 0.5949 (t70) REVERT: I 142 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7595 (mt-10) REVERT: I 516 ASP cc_start: 0.7089 (p0) cc_final: 0.6445 (p0) REVERT: I 788 SER cc_start: 0.9059 (m) cc_final: 0.8650 (p) REVERT: I 798 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7213 (mm-40) REVERT: I 1085 MET cc_start: 0.9026 (mmm) cc_final: 0.8570 (mmm) REVERT: I 1273 MET cc_start: 0.8364 (mtp) cc_final: 0.7968 (mtt) REVERT: J 96 LYS cc_start: 0.8298 (ttmt) cc_final: 0.7932 (mtpt) REVERT: J 97 VAL cc_start: 0.7501 (t) cc_final: 0.7117 (t) REVERT: J 100 GLU cc_start: 0.8162 (mp0) cc_final: 0.7663 (mp0) REVERT: J 137 ARG cc_start: 0.8528 (mtp-110) cc_final: 0.8143 (ptp90) REVERT: J 281 ARG cc_start: 0.8155 (tmm-80) cc_final: 0.7694 (tmm-80) REVERT: J 301 GLU cc_start: 0.8587 (tp30) cc_final: 0.8355 (tm-30) REVERT: J 330 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7467 (ptm) REVERT: J 484 MET cc_start: 0.8751 (mmm) cc_final: 0.8432 (mmm) REVERT: J 504 GLN cc_start: 0.7678 (mp10) cc_final: 0.7251 (mp10) REVERT: J 532 GLU cc_start: 0.7992 (tt0) cc_final: 0.7776 (tt0) REVERT: J 697 MET cc_start: 0.8170 (ttp) cc_final: 0.7906 (ttp) REVERT: J 895 CYS cc_start: 0.7247 (OUTLIER) cc_final: 0.7035 (t) REVERT: J 1123 ARG cc_start: 0.8210 (mtt180) cc_final: 0.7993 (mtp180) REVERT: J 1250 ASP cc_start: 0.8430 (m-30) cc_final: 0.8193 (m-30) REVERT: J 1254 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7832 (mt-10) REVERT: K 11 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: K 43 ASN cc_start: 0.9035 (t0) cc_final: 0.8771 (t0) outliers start: 86 outliers final: 59 residues processed: 372 average time/residue: 0.1602 time to fit residues: 98.3220 Evaluate side-chains 354 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 292 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 681 MET 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 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 1253 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 128 LEU Chi-restraints excluded: chain J residue 133 ARG 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 304 ASP Chi-restraints excluded: chain J residue 330 MET 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 505 ASP 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 895 CYS 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 J residue 1353 VAL Chi-restraints excluded: chain K residue 11 GLU 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: 0.3980 chunk 280 optimal weight: 0.0050 chunk 126 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 304 optimal weight: 9.9990 chunk 316 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 234 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- 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** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS ** 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 = 0.3771 r_free = 0.3771 target = 0.109800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.082027 restraints weight = 72076.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.084431 restraints weight = 37700.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.086020 restraints weight = 24745.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.087000 restraints weight = 19066.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.087587 restraints weight = 16358.271| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27432 Z= 0.128 Angle : 0.599 12.806 37487 Z= 0.310 Chirality : 0.042 0.293 4317 Planarity : 0.004 0.052 4558 Dihedral : 14.367 172.939 4562 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.04 % Allowed : 19.10 % Favored : 77.86 % 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: 0.72 (0.14), residues: 3152 helix: 1.39 (0.15), residues: 1134 sheet: 0.58 (0.26), residues: 399 loop : -0.14 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 133 TYR 0.038 0.002 TYR I1229 PHE 0.036 0.001 PHE I1025 TRP 0.028 0.002 TRP J 115 HIS 0.019 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (27432) covalent geometry : angle 0.59863 / 0.31 (37487) hydrogen bonds : bond 0.03990 / 4.43 ( 1140) hydrogen bonds : angle 4.84251 / 4.96 ( 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 414 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 332 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.7815 (m-80) cc_final: 0.7575 (m-80) REVERT: G 137 ASN cc_start: 0.8770 (t0) cc_final: 0.8274 (t0) REVERT: G 142 MET cc_start: 0.8376 (mtt) cc_final: 0.8017 (mtt) REVERT: G 185 TYR cc_start: 0.8687 (p90) cc_final: 0.8476 (p90) REVERT: H 104 LYS cc_start: 0.7239 (mmmt) cc_final: 0.6851 (tttt) REVERT: H 185 TYR cc_start: 0.8855 (p90) cc_final: 0.8598 (p90) REVERT: I 116 ASP cc_start: 0.6308 (p0) cc_final: 0.6050 (t70) REVERT: I 142 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7544 (mt-10) REVERT: I 516 ASP cc_start: 0.7057 (p0) cc_final: 0.6462 (p0) REVERT: I 788 SER cc_start: 0.9058 (m) cc_final: 0.8639 (p) REVERT: I 798 GLN cc_start: 0.7523 (mm-40) cc_final: 0.7069 (mm-40) REVERT: I 1085 MET cc_start: 0.8987 (mmm) cc_final: 0.8533 (mmm) REVERT: I 1273 MET cc_start: 0.8276 (mtp) cc_final: 0.8020 (mtp) REVERT: J 96 LYS cc_start: 0.8319 (ttmt) cc_final: 0.8003 (mttt) REVERT: J 97 VAL cc_start: 0.7482 (t) cc_final: 0.7054 (t) REVERT: J 100 GLU cc_start: 0.8150 (mp0) cc_final: 0.7648 (mp0) REVERT: J 115 TRP cc_start: 0.8597 (m-10) cc_final: 0.8337 (m-10) REVERT: J 137 ARG cc_start: 0.8484 (mtp-110) cc_final: 0.8118 (ptp90) REVERT: J 281 ARG cc_start: 0.8153 (tmm-80) cc_final: 0.7727 (tmm-80) REVERT: J 330 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7663 (ptm) REVERT: J 484 MET cc_start: 0.8731 (mmm) cc_final: 0.8471 (mmm) REVERT: J 504 GLN cc_start: 0.7657 (mp10) cc_final: 0.7222 (mp10) REVERT: J 532 GLU cc_start: 0.7976 (tt0) cc_final: 0.7732 (tt0) REVERT: J 642 ASP cc_start: 0.8222 (m-30) cc_final: 0.8003 (m-30) REVERT: J 697 MET cc_start: 0.8238 (ttp) cc_final: 0.7987 (ttp) REVERT: J 1123 ARG cc_start: 0.8227 (mtt180) cc_final: 0.7993 (mtp-110) REVERT: J 1250 ASP cc_start: 0.8399 (m-30) cc_final: 0.8156 (m-30) REVERT: J 1254 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7758 (mt-10) REVERT: K 11 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: K 43 ASN cc_start: 0.9035 (t0) cc_final: 0.8812 (t0) outliers start: 82 outliers final: 59 residues processed: 386 average time/residue: 0.1485 time to fit residues: 93.3177 Evaluate side-chains 364 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 303 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 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 170 VAL Chi-restraints excluded: chain I residue 195 PHE Chi-restraints excluded: chain I residue 427 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 693 LEU 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 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 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 135 ILE 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 304 ASP Chi-restraints excluded: chain J residue 330 MET 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 441 LEU Chi-restraints excluded: chain J residue 505 ASP 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 1246 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 11 GLU 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: 5.9990 chunk 305 optimal weight: 0.9990 chunk 150 optimal weight: 0.0030 chunk 217 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 234 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 chunk 227 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** 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** I1244 HIS ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 HIS ** 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 = 0.3774 r_free = 0.3774 target = 0.109962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.082793 restraints weight = 71451.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.085168 restraints weight = 37149.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.086725 restraints weight = 24321.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.087733 restraints weight = 18693.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.088299 restraints weight = 15905.732| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27432 Z= 0.124 Angle : 0.597 12.551 37487 Z= 0.308 Chirality : 0.042 0.222 4317 Planarity : 0.004 0.056 4558 Dihedral : 14.357 172.789 4562 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.70 % Allowed : 20.18 % Favored : 77.12 % 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: 0.70 (0.14), residues: 3152 helix: 1.41 (0.15), residues: 1132 sheet: 0.60 (0.26), residues: 399 loop : -0.18 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J1372 TYR 0.044 0.002 TYR I1229 PHE 0.028 0.001 PHE I1025 TRP 0.019 0.002 TRP I1276 HIS 0.024 0.001 HIS I1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (27432) covalent geometry : angle 0.59654 / 0.31 (37487) hydrogen bonds : bond 0.03898 / 4.36 ( 1140) hydrogen bonds : angle 4.78884 / 4.89 ( 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 399 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 326 time to evaluate : 0.927 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: 0.7792 (m-80) cc_final: 0.7560 (m-80) REVERT: G 137 ASN cc_start: 0.8758 (t0) cc_final: 0.8428 (t0) REVERT: G 142 MET cc_start: 0.8404 (mtt) cc_final: 0.8105 (mtt) REVERT: G 185 TYR cc_start: 0.8706 (p90) cc_final: 0.8435 (p90) REVERT: H 185 TYR cc_start: 0.8824 (p90) cc_final: 0.8568 (p90) REVERT: I 116 ASP cc_start: 0.6219 (p0) cc_final: 0.5961 (t70) REVERT: I 142 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7640 (mt-10) REVERT: I 516 ASP cc_start: 0.7083 (p0) cc_final: 0.6493 (p0) REVERT: I 524 ILE cc_start: 0.9108 (tp) cc_final: 0.8906 (tp) REVERT: I 788 SER cc_start: 0.9061 (m) cc_final: 0.8662 (p) REVERT: I 798 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7225 (mm-40) REVERT: I 1085 MET cc_start: 0.8996 (mmm) cc_final: 0.8582 (mmm) REVERT: I 1273 MET cc_start: 0.8299 (mtp) cc_final: 0.8073 (mtp) REVERT: J 96 LYS cc_start: 0.8345 (ttmt) cc_final: 0.8043 (mttt) REVERT: J 97 VAL cc_start: 0.7456 (t) cc_final: 0.7046 (t) REVERT: J 100 GLU cc_start: 0.8179 (mp0) cc_final: 0.7678 (mp0) REVERT: J 115 TRP cc_start: 0.8492 (m-10) cc_final: 0.8285 (m-10) REVERT: J 137 ARG cc_start: 0.8473 (mtp-110) cc_final: 0.8127 (ptp90) REVERT: J 281 ARG cc_start: 0.8204 (tmm-80) cc_final: 0.7798 (tmm-80) REVERT: J 352 ARG cc_start: 0.7893 (ttm-80) cc_final: 0.7406 (ttm-80) REVERT: J 484 MET cc_start: 0.8718 (mmm) cc_final: 0.8455 (mmm) REVERT: J 504 GLN cc_start: 0.7669 (mp10) cc_final: 0.7233 (mp10) REVERT: J 532 GLU cc_start: 0.7954 (tt0) cc_final: 0.7633 (tt0) REVERT: J 642 ASP cc_start: 0.8176 (m-30) cc_final: 0.7940 (m-30) REVERT: J 821 MET cc_start: 0.8845 (tpp) cc_final: 0.8581 (tpp) REVERT: J 1123 ARG cc_start: 0.8233 (mtt180) cc_final: 0.7997 (mtp-110) REVERT: J 1155 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8575 (mp) REVERT: J 1250 ASP cc_start: 0.8385 (m-30) cc_final: 0.8134 (m-30) REVERT: J 1254 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7853 (mt-10) REVERT: J 1370 MET cc_start: 0.7641 (mmp) cc_final: 0.7097 (mmt) REVERT: K 7 GLN cc_start: 0.8395 (tp40) cc_final: 0.7695 (tp40) REVERT: K 11 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8072 (mp0) outliers start: 73 outliers final: 56 residues processed: 374 average time/residue: 0.1597 time to fit residues: 97.1496 Evaluate side-chains 361 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 303 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 121 VAL 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 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 208 ILE Chi-restraints excluded: chain I residue 427 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 693 LEU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 929 ILE 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 1253 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 245 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 304 ASP 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 505 ASP 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 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 K residue 11 GLU Chi-restraints excluded: chain K residue 21 LEU 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: 20.0000 chunk 178 optimal weight: 0.7980 chunk 96 optimal weight: 0.4980 chunk 230 optimal weight: 2.9990 chunk 295 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 chunk 292 optimal weight: 8.9990 chunk 204 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** 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** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS ** 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** J1366 HIS ** 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 = 0.3766 r_free = 0.3766 target = 0.109486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.081831 restraints weight = 72515.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.084212 restraints weight = 38012.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.085785 restraints weight = 25046.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.086730 restraints weight = 19317.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.087376 restraints weight = 16589.773| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27432 Z= 0.145 Angle : 0.611 12.134 37487 Z= 0.314 Chirality : 0.042 0.210 4317 Planarity : 0.004 0.051 4558 Dihedral : 14.390 172.672 4562 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.15 % Allowed : 19.73 % Favored : 77.12 % 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: 0.66 (0.15), residues: 3152 helix: 1.39 (0.15), residues: 1138 sheet: 0.48 (0.26), residues: 386 loop : -0.19 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J1372 TYR 0.037 0.002 TYR I1229 PHE 0.025 0.001 PHE I1025 TRP 0.021 0.002 TRP I1276 HIS 0.007 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (27432) covalent geometry : angle 0.61088 / 0.31 (37487) hydrogen bonds : bond 0.03921 / 4.38 ( 1140) hydrogen bonds : angle 4.76882 / 4.88 ( 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 391 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 306 time to evaluate : 0.959 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: 0.7855 (m-80) cc_final: 0.7611 (m-80) REVERT: G 137 ASN cc_start: 0.8764 (t0) cc_final: 0.8440 (t0) REVERT: G 185 TYR cc_start: 0.8757 (p90) cc_final: 0.8463 (p90) REVERT: H 104 LYS cc_start: 0.7280 (mmmt) cc_final: 0.6930 (tttt) REVERT: H 185 TYR cc_start: 0.8843 (p90) cc_final: 0.8590 (p90) REVERT: I 116 ASP cc_start: 0.6266 (p0) cc_final: 0.5999 (t70) REVERT: I 142 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7652 (mt-10) REVERT: I 516 ASP cc_start: 0.7068 (p0) cc_final: 0.6523 (p0) REVERT: I 788 SER cc_start: 0.9097 (m) cc_final: 0.8713 (p) REVERT: I 798 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7252 (mm-40) REVERT: I 800 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8142 (ptp) REVERT: I 1085 MET cc_start: 0.8994 (mmm) cc_final: 0.8566 (mmm) REVERT: I 1273 MET cc_start: 0.8338 (mtp) cc_final: 0.8069 (mtp) REVERT: J 96 LYS cc_start: 0.8385 (ttmt) cc_final: 0.8049 (mttt) REVERT: J 97 VAL cc_start: 0.7480 (t) cc_final: 0.7049 (t) REVERT: J 100 GLU cc_start: 0.8181 (mp0) cc_final: 0.7706 (mp0) REVERT: J 115 TRP cc_start: 0.8517 (m-10) cc_final: 0.8272 (m-10) REVERT: J 180 MET cc_start: 0.7229 (tpp) cc_final: 0.6980 (tpp) REVERT: J 281 ARG cc_start: 0.8226 (tmm-80) cc_final: 0.7800 (tmm-80) REVERT: J 352 ARG cc_start: 0.7936 (ttm-80) cc_final: 0.7451 (ttm-80) REVERT: J 504 GLN cc_start: 0.7729 (mp10) cc_final: 0.7249 (mp10) REVERT: J 532 GLU cc_start: 0.7929 (tt0) cc_final: 0.7655 (tt0) REVERT: J 642 ASP cc_start: 0.8167 (m-30) cc_final: 0.7930 (m-30) REVERT: J 697 MET cc_start: 0.8058 (ttp) cc_final: 0.7760 (ttp) REVERT: J 1123 ARG cc_start: 0.8279 (mtt180) cc_final: 0.8020 (mtp-110) REVERT: J 1155 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8619 (mp) REVERT: J 1250 ASP cc_start: 0.8408 (m-30) cc_final: 0.8174 (m-30) REVERT: J 1254 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7886 (mt-10) REVERT: K 11 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: K 43 ASN cc_start: 0.9066 (t0) cc_final: 0.8816 (t0) outliers start: 85 outliers final: 64 residues processed: 365 average time/residue: 0.1576 time to fit residues: 94.1640 Evaluate side-chains 364 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 297 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 124 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 427 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 693 LEU Chi-restraints excluded: chain I residue 800 MET 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 1066 MET 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 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 237 MET Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 304 ASP 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 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 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 11 GLU 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: 5.9990 chunk 70 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 273 optimal weight: 8.9990 chunk 211 optimal weight: 0.7980 chunk 288 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 296 optimal weight: 0.0470 chunk 95 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 overall best weight: 2.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 93 GLN ** 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** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN J 477 GLN ** 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 = 0.3728 r_free = 0.3728 target = 0.107279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.079301 restraints weight = 72771.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.081649 restraints weight = 38537.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.083182 restraints weight = 25526.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.084142 restraints weight = 19777.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.084732 restraints weight = 16987.433| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 27432 Z= 0.216 Angle : 0.650 11.389 37487 Z= 0.338 Chirality : 0.043 0.221 4317 Planarity : 0.004 0.062 4558 Dihedral : 14.442 172.306 4562 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.04 % Allowed : 19.84 % Favored : 77.12 % 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 (0.15), residues: 3152 helix: 1.37 (0.15), residues: 1132 sheet: 0.41 (0.27), residues: 376 loop : -0.20 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG I1246 TYR 0.028 0.002 TYR I 291 PHE 0.026 0.002 PHE I1025 TRP 0.030 0.002 TRP I1276 HIS 0.036 0.002 HIS I1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.22 (27432) covalent geometry : angle 0.64971 / 0.34 (37487) hydrogen bonds : bond 0.04105 / 4.59 ( 1140) hydrogen bonds : angle 4.86065 / 5.00 ( 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 380 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 298 time to evaluate : 0.845 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: 0.7882 (m-80) cc_final: 0.7676 (m-80) REVERT: G 137 ASN cc_start: 0.8806 (t0) cc_final: 0.8337 (t0) REVERT: G 185 TYR cc_start: 0.8826 (p90) cc_final: 0.8589 (p90) REVERT: H 185 TYR cc_start: 0.8946 (p90) cc_final: 0.8633 (p90) REVERT: I 47 TYR cc_start: 0.4776 (m-80) cc_final: 0.4532 (m-10) REVERT: I 116 ASP cc_start: 0.6420 (p0) cc_final: 0.6109 (t70) REVERT: I 142 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7724 (mt-10) REVERT: I 315 MET cc_start: 0.7804 (mtm) cc_final: 0.7548 (mpp) REVERT: I 511 LEU cc_start: 0.8944 (mt) cc_final: 0.8612 (tp) REVERT: I 516 ASP cc_start: 0.7060 (p0) cc_final: 0.6469 (p0) REVERT: I 601 ASP cc_start: 0.8563 (t0) cc_final: 0.8050 (p0) REVERT: I 788 SER cc_start: 0.9120 (m) cc_final: 0.8839 (p) REVERT: I 798 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7352 (mm-40) REVERT: I 800 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8166 (ptp) REVERT: I 1085 MET cc_start: 0.9041 (mmm) cc_final: 0.8527 (mmm) REVERT: J 96 LYS cc_start: 0.8442 (ttmt) cc_final: 0.8126 (mttt) REVERT: J 97 VAL cc_start: 0.7549 (t) cc_final: 0.7242 (t) REVERT: J 100 GLU cc_start: 0.8162 (mp0) cc_final: 0.7742 (mp0) REVERT: J 281 ARG cc_start: 0.8295 (tmm-80) cc_final: 0.7861 (tmm-80) REVERT: J 330 MET cc_start: 0.7850 (ptm) cc_final: 0.7578 (ptm) REVERT: J 484 MET cc_start: 0.8734 (mmm) cc_final: 0.8425 (mmm) REVERT: J 504 GLN cc_start: 0.7806 (mp10) cc_final: 0.7334 (mp10) REVERT: J 532 GLU cc_start: 0.8017 (tt0) cc_final: 0.7801 (tt0) REVERT: J 642 ASP cc_start: 0.8217 (m-30) cc_final: 0.7984 (m-30) REVERT: J 697 MET cc_start: 0.8131 (ttp) cc_final: 0.7896 (ttp) REVERT: J 1123 ARG cc_start: 0.8308 (mtt180) cc_final: 0.8032 (mtp-110) REVERT: J 1155 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8669 (mp) REVERT: J 1250 ASP cc_start: 0.8466 (m-30) cc_final: 0.8254 (m-30) REVERT: J 1254 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8013 (mt-10) REVERT: J 1370 MET cc_start: 0.7908 (mmp) cc_final: 0.7248 (mmt) REVERT: K 11 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8153 (mp0) outliers start: 82 outliers final: 68 residues processed: 351 average time/residue: 0.1762 time to fit residues: 100.9110 Evaluate side-chains 360 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 289 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 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 130 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 427 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 800 MET 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 1066 MET 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 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 135 ILE 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 304 ASP 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 545 HIS 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 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 11 GLU 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 281 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 291 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 292 optimal weight: 8.9990 chunk 123 optimal weight: 0.0270 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN 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 = 0.3742 r_free = 0.3742 target = 0.108088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.080667 restraints weight = 71710.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.083025 restraints weight = 37435.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.084551 restraints weight = 24561.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.085561 restraints weight = 18897.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.085983 restraints weight = 16083.648| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27432 Z= 0.151 Angle : 0.623 12.090 37487 Z= 0.321 Chirality : 0.042 0.226 4317 Planarity : 0.004 0.050 4558 Dihedral : 14.458 171.491 4562 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.92 % Allowed : 20.33 % Favored : 76.75 % 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: 0.56 (0.15), residues: 3152 helix: 1.28 (0.15), residues: 1142 sheet: 0.35 (0.27), residues: 376 loop : -0.21 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 69 TYR 0.028 0.002 TYR I 291 PHE 0.031 0.001 PHE I1025 TRP 0.024 0.002 TRP J 115 HIS 0.013 0.001 HIS I1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (27432) covalent geometry : angle 0.62260 / 0.32 (37487) hydrogen bonds : bond 0.03956 / 4.43 ( 1140) hydrogen bonds : angle 4.79936 / 4.94 ( 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 386 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 307 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 137 ASN cc_start: 0.8756 (t0) cc_final: 0.8303 (t0) REVERT: G 185 TYR cc_start: 0.8755 (p90) cc_final: 0.8466 (p90) REVERT: H 185 TYR cc_start: 0.8937 (p90) cc_final: 0.8614 (p90) REVERT: I 47 TYR cc_start: 0.4841 (m-80) cc_final: 0.4595 (m-10) REVERT: I 116 ASP cc_start: 0.6371 (p0) cc_final: 0.6058 (t70) REVERT: I 142 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7702 (mt-10) REVERT: I 315 MET cc_start: 0.7817 (mtm) cc_final: 0.7574 (mpp) REVERT: I 422 LYS cc_start: 0.7383 (mptt) cc_final: 0.6771 (tptt) REVERT: I 429 MET cc_start: 0.8982 (mmm) cc_final: 0.8728 (mmm) REVERT: I 516 ASP cc_start: 0.7032 (p0) cc_final: 0.6437 (p0) REVERT: I 524 ILE cc_start: 0.9133 (tp) cc_final: 0.8911 (tp) REVERT: I 601 ASP cc_start: 0.8561 (t0) cc_final: 0.8061 (p0) REVERT: I 788 SER cc_start: 0.9091 (m) cc_final: 0.8766 (p) REVERT: I 798 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7351 (mm-40) REVERT: I 800 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8197 (ptp) REVERT: I 1085 MET cc_start: 0.9032 (mmm) cc_final: 0.8528 (mmm) REVERT: I 1303 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8218 (mtmm) REVERT: J 96 LYS cc_start: 0.8420 (ttmt) cc_final: 0.8120 (mttt) REVERT: J 97 VAL cc_start: 0.7540 (t) cc_final: 0.7188 (t) REVERT: J 100 GLU cc_start: 0.8159 (mp0) cc_final: 0.7723 (mp0) REVERT: J 140 TYR cc_start: 0.8185 (m-10) cc_final: 0.7664 (m-10) REVERT: J 330 MET cc_start: 0.7736 (ptm) cc_final: 0.7445 (ptm) REVERT: J 382 TYR cc_start: 0.9081 (m-80) cc_final: 0.8875 (m-80) REVERT: J 484 MET cc_start: 0.8771 (mmm) cc_final: 0.8419 (mmm) REVERT: J 504 GLN cc_start: 0.7723 (mp10) cc_final: 0.7268 (mp10) REVERT: J 1123 ARG cc_start: 0.8312 (mtt180) cc_final: 0.8044 (mtp-110) REVERT: J 1155 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8661 (mp) REVERT: J 1250 ASP cc_start: 0.8423 (m-30) cc_final: 0.8184 (m-30) REVERT: J 1254 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7898 (mt-10) REVERT: J 1370 MET cc_start: 0.7875 (mmp) cc_final: 0.7172 (mmt) REVERT: K 7 GLN cc_start: 0.8425 (tp40) cc_final: 0.7648 (tp40) REVERT: K 11 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8150 (mp0) REVERT: K 69 ARG cc_start: 0.8365 (mtp-110) cc_final: 0.7999 (ttm110) outliers start: 79 outliers final: 71 residues processed: 357 average time/residue: 0.1735 time to fit residues: 101.9683 Evaluate side-chains 372 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 297 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 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 130 MET Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 208 ILE 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 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 800 MET Chi-restraints excluded: chain I residue 835 GLU 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 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 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 135 ILE 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 304 ASP 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 545 HIS 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 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 11 GLU 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: 6.9990 chunk 247 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 273 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 271 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.108850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.081702 restraints weight = 71165.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.084047 restraints weight = 36918.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.085642 restraints weight = 24216.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.086615 restraints weight = 18469.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.087093 restraints weight = 15778.426| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27432 Z= 0.131 Angle : 0.616 12.354 37487 Z= 0.317 Chirality : 0.042 0.209 4317 Planarity : 0.004 0.051 4558 Dihedral : 14.463 171.169 4562 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.67 % Allowed : 20.96 % 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: 0.54 (0.15), residues: 3152 helix: 1.26 (0.15), residues: 1149 sheet: 0.33 (0.27), residues: 382 loop : -0.22 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 69 TYR 0.029 0.001 TYR I 291 PHE 0.045 0.002 PHE I1025 TRP 0.018 0.002 TRP I1276 HIS 0.010 0.001 HIS I1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (27432) covalent geometry : angle 0.61580 / 0.32 (37487) hydrogen bonds : bond 0.03894 / 4.37 ( 1140) hydrogen bonds : angle 4.74903 / 4.87 ( 3221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4628.25 seconds wall clock time: 81 minutes 0.68 seconds (4860.68 seconds total)