Starting phenix.real_space_refine on Sun May 25 16:48:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g2w_29683/05_2025/8g2w_29683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g2w_29683/05_2025/8g2w_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_29683/05_2025/8g2w_29683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g2w_29683/05_2025/8g2w_29683.map" model { file = "/net/cci-nas-00/data/ceres_data/8g2w_29683/05_2025/8g2w_29683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g2w_29683/05_2025/8g2w_29683.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.48s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.30, per 1000 atoms: 0.57 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: 6.73 Conformation dependent library (CDL) restraints added in 3.4 seconds 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 41 sheets defined 39.4% alpha, 15.6% beta 32 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 10.11 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: 13.06 Time building geometry restraints manager: 7.81 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=" 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 bond pdb=" N LEU J 252 " pdb=" CA LEU J 252 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.10e+01 ... (remaining 27427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 36748 1.99 - 3.98: 659 3.98 - 5.98: 62 5.98 - 7.97: 16 7.97 - 9.96: 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=" O3' DG B 22 " pdb=" C3' DG B 22 " pdb=" C2' DG B 22 " ideal model delta sigma weight residual 111.50 120.18 -8.68 1.50e+00 4.44e-01 3.35e+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 ... (remaining 37482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 16119 35.88 - 71.76: 573 71.76 - 107.64: 52 107.64 - 143.52: 5 143.52 - 179.40: 2 Dihedral angle restraints: 16751 sinusoidal: 7648 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 16748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3634 0.055 - 0.110: 582 0.110 - 0.165: 84 0.165 - 0.220: 12 0.220 - 0.275: 5 Chirality restraints: 4317 Sorted by residual: 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=" 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 -2.66 -2.40 -0.26 2.00e-01 2.50e+01 1.69e+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: 3.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 67.490 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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= 0.199 Angle : 0.633 9.959 37487 Z= 0.376 Chirality : 0.043 0.275 4317 Planarity : 0.004 0.055 4558 Dihedral : 17.336 179.396 10895 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP I 183 HIS 0.007 0.001 HIS J1366 PHE 0.018 0.001 PHE J 461 TYR 0.015 0.001 TYR J 631 ARG 0.004 0.000 ARG I 779 Details of bonding type rmsd hydrogen bonds : bond 0.17679 ( 1140) hydrogen bonds : angle 7.10663 ( 3221) covalent geometry : bond 0.00367 (27432) covalent geometry : angle 0.63293 (37487) *********************** 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 : 2.879 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: 0.8043 (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: 0.4414 time to fit residues: 466.8678 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 : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 252 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 292 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS I 46 GLN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 GLN I 490 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 684 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN ** I 811 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** ** I1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 477 GLN J 907 HIS J1195 GLN J1235 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.113783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.084928 restraints weight = 74202.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.087659 restraints weight = 35454.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.089439 restraints weight = 22478.928| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 27432 Z= 0.287 Angle : 0.714 12.453 37487 Z= 0.376 Chirality : 0.045 0.257 4317 Planarity : 0.005 0.063 4558 Dihedral : 15.954 177.375 4692 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.48 % Allowed : 14.44 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 3152 helix: 1.44 (0.15), residues: 1139 sheet: 0.80 (0.25), residues: 418 loop : 0.06 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I1276 HIS 0.013 0.002 HIS I 165 PHE 0.020 0.002 PHE I 405 TYR 0.033 0.002 TYR I1229 ARG 0.008 0.001 ARG I1034 Details of bonding type rmsd hydrogen bonds : bond 0.05005 ( 1140) hydrogen bonds : angle 5.47208 ( 3221) covalent geometry : bond 0.00635 (27432) covalent geometry : angle 0.71372 (37487) *********************** 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 443 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 376 time to evaluate : 3.222 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 137 ASN cc_start: 0.9148 (t0) cc_final: 0.8712 (t0) REVERT: G 178 SER cc_start: 0.8356 (t) cc_final: 0.8112 (p) REVERT: H 25 LYS cc_start: 0.8787 (mtpt) cc_final: 0.8581 (mtpt) REVERT: H 32 GLU cc_start: 0.7446 (tp30) cc_final: 0.7048 (mm-30) REVERT: H 185 TYR cc_start: 0.9019 (p90) cc_final: 0.8744 (p90) REVERT: I 116 ASP cc_start: 0.6908 (p0) cc_final: 0.6495 (t70) REVERT: I 142 GLU cc_start: 0.8075 (mt-10) cc_final: 0.6965 (mt-10) REVERT: I 193 ASN cc_start: 0.8225 (m110) cc_final: 0.8020 (t0) REVERT: I 213 LEU cc_start: 0.8810 (mt) cc_final: 0.8371 (mt) REVERT: I 414 ILE cc_start: 0.9180 (mm) cc_final: 0.8641 (tp) REVERT: I 422 LYS cc_start: 0.7248 (mptt) cc_final: 0.5923 (mptt) REVERT: I 516 ASP cc_start: 0.7412 (p0) cc_final: 0.6571 (p0) REVERT: I 517 GLN cc_start: 0.7917 (tt0) cc_final: 0.6910 (tt0) REVERT: I 653 MET cc_start: 0.8164 (ttp) cc_final: 0.7946 (ttp) REVERT: I 788 SER cc_start: 0.9222 (m) cc_final: 0.8845 (p) REVERT: I 798 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7214 (mm-40) REVERT: I 1085 MET cc_start: 0.9165 (mmm) cc_final: 0.8647 (mmm) REVERT: I 1273 MET cc_start: 0.8620 (mtp) cc_final: 0.8181 (mtt) REVERT: J 96 LYS cc_start: 0.8319 (ttmt) cc_final: 0.8034 (mtpt) REVERT: J 97 VAL cc_start: 0.7765 (t) cc_final: 0.7102 (t) REVERT: J 100 GLU cc_start: 0.8248 (mp0) cc_final: 0.7669 (mp0) REVERT: J 281 ARG cc_start: 0.8176 (tmm-80) cc_final: 0.7818 (tmm-80) REVERT: J 301 GLU cc_start: 0.8580 (tp30) cc_final: 0.8330 (tm-30) REVERT: J 375 GLU cc_start: 0.7967 (tp30) cc_final: 0.7209 (tp30) REVERT: J 656 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7738 (mt-10) REVERT: J 835 LEU cc_start: 0.8485 (tp) cc_final: 0.8218 (tp) REVERT: J 1123 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7994 (mmm160) REVERT: J 1254 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8101 (mt-10) REVERT: K 11 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: K 43 ASN cc_start: 0.9080 (t0) cc_final: 0.8796 (t0) REVERT: K 55 GLU cc_start: 0.8662 (tt0) cc_final: 0.8423 (tt0) REVERT: K 60 ASN cc_start: 0.9066 (p0) cc_final: 0.8861 (p0) outliers start: 67 outliers final: 45 residues processed: 419 average time/residue: 0.3907 time to fit residues: 257.9480 Evaluate side-chains 335 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 289 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 692 THR Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 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 1076 ILE 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 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 262 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 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 573 THR Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 740 LEU 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 236 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 316 optimal weight: 0.4980 chunk 31 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 148 optimal weight: 0.2980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 450 ASN I 490 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN I1209 GLN I1244 HIS ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN J1010 GLN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.116352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.088197 restraints weight = 74044.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.090989 restraints weight = 35098.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.092789 restraints weight = 22135.865| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2804 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= 0.149 Angle : 0.607 13.751 37487 Z= 0.317 Chirality : 0.042 0.210 4317 Planarity : 0.004 0.057 4558 Dihedral : 15.953 176.392 4692 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.15 % Allowed : 16.18 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.14), residues: 3152 helix: 1.43 (0.15), residues: 1133 sheet: 0.60 (0.26), residues: 395 loop : 0.06 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 580 HIS 0.014 0.001 HIS I 165 PHE 0.020 0.002 PHE I1025 TYR 0.026 0.002 TYR H 177 ARG 0.012 0.001 ARG J 978 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 1140) hydrogen bonds : angle 5.10879 ( 3221) covalent geometry : bond 0.00332 (27432) covalent geometry : angle 0.60745 (37487) *********************** 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 454 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 369 time to evaluate : 2.827 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 137 ASN cc_start: 0.9175 (t0) cc_final: 0.8711 (t0) REVERT: G 178 SER cc_start: 0.8439 (t) cc_final: 0.8172 (p) REVERT: G 185 TYR cc_start: 0.8681 (p90) cc_final: 0.8447 (p90) REVERT: H 32 GLU cc_start: 0.7501 (tp30) cc_final: 0.7271 (mm-30) REVERT: H 185 TYR cc_start: 0.8964 (p90) cc_final: 0.8675 (p90) REVERT: I 116 ASP cc_start: 0.6849 (p0) cc_final: 0.6462 (t70) REVERT: I 142 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7725 (mt-10) REVERT: I 193 ASN cc_start: 0.8177 (m110) cc_final: 0.7955 (t0) REVERT: I 239 MET cc_start: 0.4179 (tmm) cc_final: 0.3955 (tmm) REVERT: I 422 LYS cc_start: 0.7161 (mptt) cc_final: 0.6800 (mptt) REVERT: I 516 ASP cc_start: 0.7298 (p0) cc_final: 0.6655 (p0) REVERT: I 785 ASP cc_start: 0.6903 (m-30) cc_final: 0.6413 (p0) REVERT: I 788 SER cc_start: 0.9087 (m) cc_final: 0.8681 (p) REVERT: I 798 GLN cc_start: 0.7759 (mm-40) cc_final: 0.7135 (mm-40) REVERT: I 811 ASN cc_start: 0.9148 (OUTLIER) cc_final: 0.8818 (p0) REVERT: I 1040 ASP cc_start: 0.7015 (t70) cc_final: 0.6668 (t70) REVERT: I 1041 ASP cc_start: 0.8549 (p0) cc_final: 0.8326 (p0) REVERT: I 1085 MET cc_start: 0.9171 (mmm) cc_final: 0.8675 (mmm) REVERT: I 1229 TYR cc_start: 0.9012 (m-80) cc_final: 0.8769 (m-10) REVERT: I 1273 MET cc_start: 0.8553 (mtp) cc_final: 0.8093 (mtt) REVERT: J 96 LYS cc_start: 0.8390 (ttmt) cc_final: 0.7914 (mtpt) REVERT: J 97 VAL cc_start: 0.7657 (t) cc_final: 0.7187 (t) REVERT: J 100 GLU cc_start: 0.8260 (mp0) cc_final: 0.7648 (mp0) REVERT: J 133 ARG cc_start: 0.7839 (mpt180) cc_final: 0.7632 (mpt180) REVERT: J 137 ARG cc_start: 0.8447 (mtp-110) cc_final: 0.7910 (ptp90) REVERT: J 301 GLU cc_start: 0.8561 (tp30) cc_final: 0.8232 (tm-30) REVERT: J 382 TYR cc_start: 0.9229 (m-10) cc_final: 0.9014 (m-80) REVERT: J 497 GLU cc_start: 0.8173 (pm20) cc_final: 0.7908 (pm20) REVERT: J 504 GLN cc_start: 0.7724 (mp10) cc_final: 0.7333 (mp10) REVERT: J 656 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7669 (mt-10) REVERT: J 697 MET cc_start: 0.8153 (ttp) cc_final: 0.7903 (ttp) REVERT: J 799 ARG cc_start: 0.8931 (mtm110) cc_final: 0.8128 (mtm110) REVERT: J 1123 ARG cc_start: 0.8416 (mtt180) cc_final: 0.7999 (mtp-110) REVERT: J 1254 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8023 (mt-10) REVERT: K 10 VAL cc_start: 0.9148 (OUTLIER) cc_final: 0.8909 (m) REVERT: K 11 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: K 43 ASN cc_start: 0.9179 (t0) cc_final: 0.8903 (t0) outliers start: 85 outliers final: 47 residues processed: 428 average time/residue: 0.3560 time to fit residues: 245.1531 Evaluate side-chains 365 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 315 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 206 GLU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 39 ILE 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 442 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 811 ASN Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1076 ILE 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 1253 LEU Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 20 ILE 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 120 LEU Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 237 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 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 978 ARG Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 41 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 242 optimal weight: 5.9990 chunk 286 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 94 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 146 optimal weight: 10.0000 chunk 278 optimal weight: 5.9990 chunk 137 optimal weight: 0.0980 chunk 248 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 HIS I 165 HIS I 490 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 628 HIS ** I 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 811 ASN ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 232 ASN J1010 GLN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.108422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.081537 restraints weight = 71150.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.083850 restraints weight = 36907.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.085402 restraints weight = 24055.630| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27432 Z= 0.144 Angle : 0.590 13.781 37487 Z= 0.307 Chirality : 0.041 0.255 4317 Planarity : 0.004 0.055 4558 Dihedral : 15.923 174.992 4692 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.44 % Allowed : 17.36 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3152 helix: 1.43 (0.15), residues: 1138 sheet: 0.55 (0.26), residues: 403 loop : -0.03 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 580 HIS 0.013 0.001 HIS I 165 PHE 0.028 0.001 PHE I1025 TYR 0.032 0.002 TYR H 177 ARG 0.010 0.000 ARG J 978 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 1140) hydrogen bonds : angle 4.90475 ( 3221) covalent geometry : bond 0.00322 (27432) covalent geometry : angle 0.59034 (37487) *********************** 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 436 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 343 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 137 ASN cc_start: 0.8875 (t0) cc_final: 0.8365 (t0) REVERT: G 185 TYR cc_start: 0.8668 (p90) cc_final: 0.8447 (p90) REVERT: H 185 TYR cc_start: 0.8900 (p90) cc_final: 0.8590 (p90) REVERT: I 116 ASP cc_start: 0.6338 (p0) cc_final: 0.6058 (t70) REVERT: I 142 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7653 (mt-10) REVERT: I 516 ASP cc_start: 0.7077 (p0) cc_final: 0.6506 (p0) REVERT: I 788 SER cc_start: 0.9092 (m) cc_final: 0.8659 (p) REVERT: I 798 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7123 (mm-40) REVERT: I 1040 ASP cc_start: 0.6515 (t70) cc_final: 0.6185 (t70) REVERT: I 1041 ASP cc_start: 0.8387 (p0) cc_final: 0.8148 (p0) REVERT: I 1065 LYS cc_start: 0.8810 (tttt) cc_final: 0.8606 (tttm) REVERT: I 1085 MET cc_start: 0.9038 (mmm) cc_final: 0.8563 (mmm) REVERT: I 1273 MET cc_start: 0.8251 (mtp) cc_final: 0.7869 (mtt) REVERT: J 96 LYS cc_start: 0.8346 (ttmt) cc_final: 0.7942 (mtpt) REVERT: J 97 VAL cc_start: 0.7584 (t) cc_final: 0.7184 (t) REVERT: J 100 GLU cc_start: 0.8090 (mp0) cc_final: 0.7647 (mp0) REVERT: J 137 ARG cc_start: 0.8392 (mtp-110) cc_final: 0.8063 (ptp90) REVERT: J 301 GLU cc_start: 0.8648 (tp30) cc_final: 0.8265 (tm-30) REVERT: J 330 MET cc_start: 0.7640 (ttp) cc_final: 0.7310 (ptm) REVERT: J 352 ARG cc_start: 0.7649 (ttm-80) cc_final: 0.7401 (ttm-80) REVERT: J 398 LYS cc_start: 0.8313 (mttt) cc_final: 0.7906 (mtmm) REVERT: J 504 GLN cc_start: 0.7687 (mp10) cc_final: 0.7281 (mp10) REVERT: J 697 MET cc_start: 0.8185 (ttp) cc_final: 0.7938 (ttp) REVERT: J 1189 MET cc_start: 0.7822 (mmt) cc_final: 0.7300 (tpt) REVERT: J 1254 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7839 (mt-10) REVERT: K 7 GLN cc_start: 0.8408 (tp40) cc_final: 0.7768 (tp40) outliers start: 93 outliers final: 62 residues processed: 408 average time/residue: 0.3744 time to fit residues: 245.6005 Evaluate side-chains 360 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 298 time to evaluate : 2.964 ------------------------------------------------------------------------------- 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 130 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 20 ILE 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 120 LEU Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 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 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 1351 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 60 optimal weight: 4.9990 chunk 210 optimal weight: 0.3980 chunk 219 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 303 optimal weight: 7.9990 chunk 276 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 286 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 HIS ** I 618 GLN ** 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 ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1264 GLN ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.109199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.081563 restraints weight = 71543.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.083954 restraints weight = 37175.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.085551 restraints weight = 24375.002| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27432 Z= 0.127 Angle : 0.580 13.670 37487 Z= 0.300 Chirality : 0.041 0.244 4317 Planarity : 0.004 0.054 4558 Dihedral : 15.899 174.598 4692 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.41 % Allowed : 19.03 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 3152 helix: 1.37 (0.15), residues: 1145 sheet: 0.51 (0.26), residues: 403 loop : -0.10 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I1276 HIS 0.014 0.001 HIS I 165 PHE 0.036 0.002 PHE I1025 TYR 0.032 0.001 TYR H 177 ARG 0.005 0.000 ARG K 69 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 1140) hydrogen bonds : angle 4.78289 ( 3221) covalent geometry : bond 0.00280 (27432) covalent geometry : angle 0.57961 (37487) *********************** 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 444 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 352 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.8136 (m-80) cc_final: 0.7598 (t80) REVERT: G 137 ASN cc_start: 0.8899 (t0) cc_final: 0.8491 (t0) REVERT: H 104 LYS cc_start: 0.7236 (mmmt) cc_final: 0.6938 (tttt) REVERT: H 185 TYR cc_start: 0.8857 (p90) cc_final: 0.8580 (p90) REVERT: I 116 ASP cc_start: 0.6504 (p0) cc_final: 0.6206 (t70) REVERT: I 142 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7659 (mt-10) REVERT: I 516 ASP cc_start: 0.7063 (p0) cc_final: 0.6511 (p0) REVERT: I 788 SER cc_start: 0.9074 (m) cc_final: 0.8654 (p) REVERT: I 798 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7297 (mm-40) REVERT: I 1040 ASP cc_start: 0.6486 (t70) cc_final: 0.6156 (t0) REVERT: I 1041 ASP cc_start: 0.8302 (p0) cc_final: 0.7853 (p0) REVERT: I 1085 MET cc_start: 0.9037 (mmm) cc_final: 0.8535 (mmm) REVERT: I 1273 MET cc_start: 0.8285 (mtp) cc_final: 0.8082 (mtp) REVERT: J 96 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7994 (mtpt) REVERT: J 97 VAL cc_start: 0.7481 (t) cc_final: 0.7004 (t) REVERT: J 100 GLU cc_start: 0.8112 (mp0) cc_final: 0.7650 (mp0) REVERT: J 137 ARG cc_start: 0.8368 (mtp-110) cc_final: 0.8054 (ptp90) REVERT: J 140 TYR cc_start: 0.7952 (m-10) cc_final: 0.7670 (m-10) REVERT: J 281 ARG cc_start: 0.8244 (tmm-80) cc_final: 0.7897 (tmm-80) REVERT: J 301 GLU cc_start: 0.8643 (tp30) cc_final: 0.8320 (tm-30) REVERT: J 330 MET cc_start: 0.7628 (ttp) cc_final: 0.7287 (ptm) REVERT: J 504 GLN cc_start: 0.7745 (mp10) cc_final: 0.7313 (mp10) REVERT: J 532 GLU cc_start: 0.8036 (tt0) cc_final: 0.7793 (tt0) REVERT: J 1025 MET cc_start: 0.8306 (mpp) cc_final: 0.8098 (mpp) REVERT: J 1155 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8607 (mp) REVERT: J 1254 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7824 (mt-10) REVERT: K 43 ASN cc_start: 0.8991 (t0) cc_final: 0.8759 (t0) outliers start: 92 outliers final: 58 residues processed: 414 average time/residue: 0.3993 time to fit residues: 265.6241 Evaluate side-chains 361 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 302 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 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 611 GLU Chi-restraints excluded: chain I residue 692 THR Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS 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 K residue 31 GLN Chi-restraints excluded: chain K residue 48 VAL 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 112 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 272 optimal weight: 20.0000 chunk 219 optimal weight: 6.9990 chunk 283 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 194 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 251 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS I 165 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN I1061 GLN ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS K 15 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.109769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.082529 restraints weight = 71842.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.084985 restraints weight = 37125.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086569 restraints weight = 24184.285| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27432 Z= 0.133 Angle : 0.584 12.601 37487 Z= 0.301 Chirality : 0.041 0.212 4317 Planarity : 0.004 0.052 4558 Dihedral : 15.911 174.519 4692 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.37 % Allowed : 20.21 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 3152 helix: 1.34 (0.15), residues: 1155 sheet: 0.42 (0.27), residues: 383 loop : -0.14 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 580 HIS 0.013 0.001 HIS I 165 PHE 0.027 0.001 PHE I1025 TYR 0.044 0.002 TYR I1229 ARG 0.009 0.000 ARG J1372 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 1140) hydrogen bonds : angle 4.72106 ( 3221) covalent geometry : bond 0.00302 (27432) covalent geometry : angle 0.58413 (37487) *********************** 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 417 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 326 time to evaluate : 2.881 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: H 185 TYR cc_start: 0.8844 (p90) cc_final: 0.8634 (p90) REVERT: I 116 ASP cc_start: 0.6472 (p0) cc_final: 0.6223 (t70) REVERT: I 516 ASP cc_start: 0.7089 (p0) cc_final: 0.6561 (p0) REVERT: I 601 ASP cc_start: 0.8525 (t0) cc_final: 0.8092 (p0) REVERT: I 788 SER cc_start: 0.9194 (m) cc_final: 0.8779 (p) REVERT: I 1040 ASP cc_start: 0.6422 (t70) cc_final: 0.6177 (t70) REVERT: I 1085 MET cc_start: 0.9000 (mmm) cc_final: 0.8527 (mmm) REVERT: I 1273 MET cc_start: 0.8363 (mtp) cc_final: 0.8134 (mtp) REVERT: J 96 LYS cc_start: 0.8278 (ttmt) cc_final: 0.8031 (mttt) REVERT: J 97 VAL cc_start: 0.7496 (t) cc_final: 0.7038 (t) REVERT: J 100 GLU cc_start: 0.8131 (mp0) cc_final: 0.7664 (mp0) REVERT: J 136 GLU cc_start: 0.8272 (tp30) cc_final: 0.7084 (tp30) REVERT: J 137 ARG cc_start: 0.8252 (mtp-110) cc_final: 0.8020 (ptp90) REVERT: J 140 TYR cc_start: 0.7422 (m-10) cc_final: 0.7114 (m-10) REVERT: J 281 ARG cc_start: 0.8287 (tmm-80) cc_final: 0.7944 (tmm-80) REVERT: J 301 GLU cc_start: 0.8513 (tp30) cc_final: 0.8281 (tm-30) REVERT: J 330 MET cc_start: 0.7559 (ttp) cc_final: 0.7212 (ptm) REVERT: J 382 TYR cc_start: 0.9044 (m-80) cc_final: 0.8834 (m-80) REVERT: J 504 GLN cc_start: 0.7745 (mp10) cc_final: 0.7306 (mp10) REVERT: J 642 ASP cc_start: 0.8178 (m-30) cc_final: 0.7961 (m-30) REVERT: J 1025 MET cc_start: 0.8327 (mpp) cc_final: 0.8121 (mpp) REVERT: J 1155 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8621 (mp) REVERT: J 1254 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7760 (mt-10) outliers start: 91 outliers final: 70 residues processed: 390 average time/residue: 0.3596 time to fit residues: 227.7510 Evaluate side-chains 363 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 292 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 54 CYS 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 384 LEU Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1296 ASP Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 343 LEU 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 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 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 41 GLU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 60 ASN 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 26 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 288 optimal weight: 5.9990 chunk 312 optimal weight: 4.9990 chunk 247 optimal weight: 6.9990 chunk 131 optimal weight: 0.0070 chunk 184 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 242 optimal weight: 8.9990 chunk 183 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 overall best weight: 3.0804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 450 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.106069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.078536 restraints weight = 71794.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.080829 restraints weight = 37628.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.082349 restraints weight = 24846.055| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27432 Z= 0.220 Angle : 0.625 11.682 37487 Z= 0.326 Chirality : 0.042 0.222 4317 Planarity : 0.004 0.051 4558 Dihedral : 15.961 174.949 4692 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.81 % Allowed : 20.10 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 3152 helix: 1.38 (0.15), residues: 1139 sheet: 0.31 (0.27), residues: 384 loop : -0.15 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 115 HIS 0.013 0.001 HIS I 165 PHE 0.031 0.002 PHE I1025 TYR 0.046 0.002 TYR I1229 ARG 0.008 0.001 ARG I1034 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 1140) hydrogen bonds : angle 4.82446 ( 3221) covalent geometry : bond 0.00494 (27432) covalent geometry : angle 0.62522 (37487) *********************** 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 396 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 293 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.8590 (m-80) cc_final: 0.8000 (t80) REVERT: G 137 ASN cc_start: 0.8824 (t0) cc_final: 0.8357 (t0) REVERT: H 185 TYR cc_start: 0.9000 (p90) cc_final: 0.8715 (p90) REVERT: I 116 ASP cc_start: 0.6623 (p0) cc_final: 0.6279 (t70) REVERT: I 414 ILE cc_start: 0.9083 (mm) cc_final: 0.8708 (tp) REVERT: I 510 GLN cc_start: 0.8591 (tt0) cc_final: 0.8318 (tt0) REVERT: I 516 ASP cc_start: 0.7123 (p0) cc_final: 0.6561 (p0) REVERT: I 601 ASP cc_start: 0.8607 (t0) cc_final: 0.8075 (p0) REVERT: I 788 SER cc_start: 0.9234 (m) cc_final: 0.8950 (p) REVERT: I 1085 MET cc_start: 0.9030 (mmm) cc_final: 0.8484 (mmm) REVERT: J 96 LYS cc_start: 0.8342 (ttmt) cc_final: 0.8133 (mttt) REVERT: J 97 VAL cc_start: 0.7606 (t) cc_final: 0.7003 (t) REVERT: J 100 GLU cc_start: 0.8125 (mp0) cc_final: 0.7731 (mp0) REVERT: J 136 GLU cc_start: 0.8400 (tp30) cc_final: 0.7049 (tp30) REVERT: J 137 ARG cc_start: 0.8294 (mtp-110) cc_final: 0.8052 (ptp90) REVERT: J 140 TYR cc_start: 0.7566 (m-10) cc_final: 0.7162 (m-10) REVERT: J 281 ARG cc_start: 0.8365 (tmm-80) cc_final: 0.7902 (tmm-80) REVERT: J 301 GLU cc_start: 0.8580 (tp30) cc_final: 0.8311 (tm-30) REVERT: J 382 TYR cc_start: 0.9125 (m-80) cc_final: 0.8923 (m-80) REVERT: J 398 LYS cc_start: 0.8328 (mptt) cc_final: 0.8101 (mppt) REVERT: J 504 GLN cc_start: 0.7788 (mp10) cc_final: 0.7349 (mp10) REVERT: J 698 MET cc_start: 0.9275 (mmm) cc_final: 0.8989 (tpp) REVERT: J 699 ASP cc_start: 0.7980 (m-30) cc_final: 0.7723 (t0) REVERT: J 799 ARG cc_start: 0.8915 (mtm110) cc_final: 0.8085 (mtm110) REVERT: J 1025 MET cc_start: 0.8391 (mpp) cc_final: 0.8185 (mpp) REVERT: J 1155 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8702 (mp) REVERT: J 1254 GLU cc_start: 0.8249 (mt-10) cc_final: 0.8024 (mt-10) REVERT: J 1370 MET cc_start: 0.7819 (mmp) cc_final: 0.7186 (mmt) outliers start: 103 outliers final: 78 residues processed: 368 average time/residue: 0.3564 time to fit residues: 214.1614 Evaluate side-chains 360 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 281 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 384 LEU 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 692 THR Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 343 LEU 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 453 VAL 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 751 ASP Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 41 GLU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 68 optimal weight: 6.9990 chunk 124 optimal weight: 0.0970 chunk 299 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 273 optimal weight: 8.9990 chunk 307 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 165 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.113216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.085203 restraints weight = 74377.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.088189 restraints weight = 36062.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.089219 restraints weight = 21184.155| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27432 Z= 0.209 Angle : 0.628 14.127 37487 Z= 0.325 Chirality : 0.042 0.220 4317 Planarity : 0.004 0.050 4558 Dihedral : 16.034 174.080 4692 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.48 % Allowed : 20.44 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3152 helix: 1.27 (0.15), residues: 1154 sheet: 0.38 (0.27), residues: 372 loop : -0.27 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 115 HIS 0.023 0.001 HIS G 23 PHE 0.043 0.002 PHE I1025 TYR 0.034 0.002 TYR I1229 ARG 0.009 0.001 ARG I1246 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 1140) hydrogen bonds : angle 4.85725 ( 3221) covalent geometry : bond 0.00473 (27432) covalent geometry : angle 0.62786 (37487) *********************** 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 386 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 292 time to evaluate : 2.798 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: 0.8665 (m-80) cc_final: 0.8060 (t80) REVERT: G 137 ASN cc_start: 0.8997 (t0) cc_final: 0.8570 (t0) REVERT: H 185 TYR cc_start: 0.9064 (p90) cc_final: 0.8768 (p90) REVERT: I 116 ASP cc_start: 0.7446 (p0) cc_final: 0.7094 (t70) REVERT: I 414 ILE cc_start: 0.9124 (mm) cc_final: 0.8697 (tp) REVERT: I 422 LYS cc_start: 0.7401 (mptt) cc_final: 0.6729 (tptt) REVERT: I 516 ASP cc_start: 0.7330 (p0) cc_final: 0.6771 (p0) REVERT: I 517 GLN cc_start: 0.8149 (tt0) cc_final: 0.7773 (tt0) REVERT: I 601 ASP cc_start: 0.8655 (t0) cc_final: 0.8090 (p0) REVERT: I 741 MET cc_start: 0.8787 (ptm) cc_final: 0.8561 (ptm) REVERT: I 788 SER cc_start: 0.9240 (m) cc_final: 0.8931 (p) REVERT: I 1085 MET cc_start: 0.9153 (mmm) cc_final: 0.8604 (mmm) REVERT: J 96 LYS cc_start: 0.8339 (ttmt) cc_final: 0.8101 (mttt) REVERT: J 97 VAL cc_start: 0.7417 (t) cc_final: 0.6801 (t) REVERT: J 100 GLU cc_start: 0.8197 (mp0) cc_final: 0.7612 (mp0) REVERT: J 136 GLU cc_start: 0.8716 (tp30) cc_final: 0.7228 (tp30) REVERT: J 137 ARG cc_start: 0.8410 (mtp-110) cc_final: 0.8077 (ptp90) REVERT: J 140 TYR cc_start: 0.7667 (m-10) cc_final: 0.7196 (m-10) REVERT: J 281 ARG cc_start: 0.8559 (tmm-80) cc_final: 0.8052 (tmm-80) REVERT: J 301 GLU cc_start: 0.8652 (tp30) cc_final: 0.8306 (tm-30) REVERT: J 330 MET cc_start: 0.8051 (ttp) cc_final: 0.7244 (ptm) REVERT: J 382 TYR cc_start: 0.9222 (m-80) cc_final: 0.8982 (m-80) REVERT: J 398 LYS cc_start: 0.8313 (mptt) cc_final: 0.8061 (mppt) REVERT: J 504 GLN cc_start: 0.7838 (mp10) cc_final: 0.7396 (mp10) REVERT: J 699 ASP cc_start: 0.8147 (m-30) cc_final: 0.7813 (t0) REVERT: J 799 ARG cc_start: 0.8985 (mtm110) cc_final: 0.8010 (mtm110) REVERT: J 821 MET cc_start: 0.9005 (tpp) cc_final: 0.8734 (tpp) REVERT: J 1025 MET cc_start: 0.8488 (mpp) cc_final: 0.8285 (mpp) REVERT: J 1155 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8601 (mp) outliers start: 94 outliers final: 78 residues processed: 361 average time/residue: 0.3529 time to fit residues: 207.8815 Evaluate side-chains 361 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 282 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 531 SER Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 692 THR Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1230 THR Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 299 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 141 optimal weight: 0.0570 chunk 81 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 254 optimal weight: 0.6980 chunk 202 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS K 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.115531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.088231 restraints weight = 74964.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.091364 restraints weight = 36083.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.092330 restraints weight = 21183.881| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3911 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= 0.130 Angle : 0.602 12.840 37487 Z= 0.309 Chirality : 0.041 0.212 4317 Planarity : 0.004 0.050 4558 Dihedral : 16.040 172.918 4692 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.81 % Allowed : 21.55 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3152 helix: 1.30 (0.15), residues: 1147 sheet: 0.40 (0.27), residues: 372 loop : -0.22 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 115 HIS 0.004 0.001 HIS G 23 PHE 0.040 0.001 PHE I1025 TYR 0.037 0.001 TYR I1229 ARG 0.008 0.000 ARG K 69 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 1140) hydrogen bonds : angle 4.71774 ( 3221) covalent geometry : bond 0.00296 (27432) covalent geometry : angle 0.60193 (37487) *********************** 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 395 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 319 time to evaluate : 2.929 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: 0.8599 (m-80) cc_final: 0.8036 (t80) REVERT: G 137 ASN cc_start: 0.9020 (t0) cc_final: 0.8744 (t0) REVERT: H 104 LYS cc_start: 0.7425 (mmmt) cc_final: 0.7022 (tttt) REVERT: H 185 TYR cc_start: 0.9018 (p90) cc_final: 0.8744 (p90) REVERT: I 116 ASP cc_start: 0.7571 (p0) cc_final: 0.7235 (t70) REVERT: I 213 LEU cc_start: 0.8848 (mt) cc_final: 0.8603 (mt) REVERT: I 414 ILE cc_start: 0.9105 (mm) cc_final: 0.8661 (tp) REVERT: I 422 LYS cc_start: 0.7377 (mptt) cc_final: 0.6042 (mptt) REVERT: I 516 ASP cc_start: 0.7285 (p0) cc_final: 0.6512 (p0) REVERT: I 517 GLN cc_start: 0.8047 (tt0) cc_final: 0.7648 (tt0) REVERT: I 601 ASP cc_start: 0.8597 (t0) cc_final: 0.8058 (p0) REVERT: I 761 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8311 (mm-40) REVERT: I 788 SER cc_start: 0.9226 (m) cc_final: 0.8823 (p) REVERT: I 1040 ASP cc_start: 0.6857 (t70) cc_final: 0.6560 (t0) REVERT: I 1085 MET cc_start: 0.9114 (mmm) cc_final: 0.8538 (mmm) REVERT: J 96 LYS cc_start: 0.8260 (ttmt) cc_final: 0.7926 (mttt) REVERT: J 97 VAL cc_start: 0.7392 (t) cc_final: 0.6934 (t) REVERT: J 100 GLU cc_start: 0.8174 (mp0) cc_final: 0.7599 (mp0) REVERT: J 136 GLU cc_start: 0.8764 (tp30) cc_final: 0.7328 (tp30) REVERT: J 137 ARG cc_start: 0.8350 (mtp-110) cc_final: 0.8038 (ptp90) REVERT: J 140 TYR cc_start: 0.7593 (m-10) cc_final: 0.7221 (m-10) REVERT: J 301 GLU cc_start: 0.8621 (tp30) cc_final: 0.8255 (tm-30) REVERT: J 382 TYR cc_start: 0.9213 (m-80) cc_final: 0.8935 (m-80) REVERT: J 398 LYS cc_start: 0.8320 (mptt) cc_final: 0.8034 (mppt) REVERT: J 504 GLN cc_start: 0.7754 (mp10) cc_final: 0.7251 (mp10) REVERT: J 821 MET cc_start: 0.8996 (tpp) cc_final: 0.8764 (tpp) REVERT: J 826 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7953 (mp) REVERT: J 1025 MET cc_start: 0.8438 (mpp) cc_final: 0.8236 (mpp) REVERT: J 1155 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8552 (mp) REVERT: J 1254 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8050 (mt-10) REVERT: J 1370 MET cc_start: 0.7979 (mmp) cc_final: 0.7397 (mmt) REVERT: K 59 ILE cc_start: 0.8374 (mt) cc_final: 0.8131 (mm) outliers start: 76 outliers final: 64 residues processed: 373 average time/residue: 0.3590 time to fit residues: 218.4929 Evaluate side-chains 363 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 297 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 384 LEU 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 565 GLU Chi-restraints excluded: chain I residue 611 GLU Chi-restraints excluded: chain I residue 692 THR Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 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 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 J residue 1366 HIS Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 161 optimal weight: 0.7980 chunk 287 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 286 optimal weight: 20.0000 chunk 244 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 80 optimal weight: 0.0470 chunk 108 optimal weight: 7.9990 chunk 309 optimal weight: 2.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS H 227 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 686 GLN ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS K 15 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.116534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089547 restraints weight = 74672.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.092829 restraints weight = 35891.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.093752 restraints weight = 20433.822| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4058 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= 0.125 Angle : 0.602 12.516 37487 Z= 0.309 Chirality : 0.041 0.213 4317 Planarity : 0.004 0.051 4558 Dihedral : 15.999 172.863 4692 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.52 % Allowed : 22.14 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.15), residues: 3152 helix: 1.30 (0.15), residues: 1155 sheet: 0.45 (0.28), residues: 361 loop : -0.25 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 580 HIS 0.022 0.001 HIS J1366 PHE 0.037 0.001 PHE I1025 TYR 0.034 0.001 TYR I1229 ARG 0.009 0.000 ARG K 69 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 1140) hydrogen bonds : angle 4.64166 ( 3221) covalent geometry : bond 0.00280 (27432) covalent geometry : angle 0.60173 (37487) ********************** 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 379 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 311 time to evaluate : 2.999 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: 0.8556 (m-80) cc_final: 0.8119 (t80) REVERT: G 137 ASN cc_start: 0.8989 (t0) cc_final: 0.8718 (t0) REVERT: H 185 TYR cc_start: 0.9004 (p90) cc_final: 0.8773 (p90) REVERT: I 116 ASP cc_start: 0.7592 (p0) cc_final: 0.7232 (t70) REVERT: I 213 LEU cc_start: 0.8809 (mt) cc_final: 0.8601 (mt) REVERT: I 414 ILE cc_start: 0.9115 (mm) cc_final: 0.8668 (tp) REVERT: I 422 LYS cc_start: 0.7402 (mptt) cc_final: 0.6086 (mptt) REVERT: I 429 MET cc_start: 0.9119 (mmm) cc_final: 0.8815 (mmm) REVERT: I 516 ASP cc_start: 0.7324 (p0) cc_final: 0.6794 (p0) REVERT: I 517 GLN cc_start: 0.7979 (tt0) cc_final: 0.7516 (tt0) REVERT: I 601 ASP cc_start: 0.8570 (t0) cc_final: 0.8033 (p0) REVERT: I 788 SER cc_start: 0.9248 (m) cc_final: 0.8796 (p) REVERT: I 1040 ASP cc_start: 0.6766 (t70) cc_final: 0.6478 (t0) REVERT: I 1085 MET cc_start: 0.9106 (mmm) cc_final: 0.8673 (mmm) REVERT: J 96 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7975 (mttt) REVERT: J 97 VAL cc_start: 0.7359 (t) cc_final: 0.6914 (t) REVERT: J 100 GLU cc_start: 0.8181 (mp0) cc_final: 0.7667 (mp0) REVERT: J 115 TRP cc_start: 0.8683 (m-10) cc_final: 0.8341 (m-10) REVERT: J 136 GLU cc_start: 0.8775 (tp30) cc_final: 0.7685 (tp30) REVERT: J 137 ARG cc_start: 0.8319 (mtp-110) cc_final: 0.8044 (ptp90) REVERT: J 140 TYR cc_start: 0.7521 (m-10) cc_final: 0.7262 (m-10) REVERT: J 301 GLU cc_start: 0.8620 (tp30) cc_final: 0.8274 (tm-30) REVERT: J 330 MET cc_start: 0.8010 (ttp) cc_final: 0.7209 (ptm) REVERT: J 382 TYR cc_start: 0.9212 (m-80) cc_final: 0.8948 (m-80) REVERT: J 398 LYS cc_start: 0.8332 (mptt) cc_final: 0.8050 (mppt) REVERT: J 504 GLN cc_start: 0.7696 (mp10) cc_final: 0.7201 (mp10) REVERT: J 821 MET cc_start: 0.8976 (tpp) cc_final: 0.8773 (tpp) REVERT: J 1025 MET cc_start: 0.8435 (mpp) cc_final: 0.8231 (mpp) REVERT: J 1155 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8571 (mp) REVERT: J 1370 MET cc_start: 0.8014 (mmp) cc_final: 0.7554 (mmt) REVERT: K 15 ASN cc_start: 0.8313 (m110) cc_final: 0.7802 (m-40) REVERT: K 59 ILE cc_start: 0.8329 (mt) cc_final: 0.8105 (mm) REVERT: K 69 ARG cc_start: 0.8752 (mtp-110) cc_final: 0.8437 (ttm110) outliers start: 68 outliers final: 57 residues processed: 359 average time/residue: 0.3623 time to fit residues: 211.8567 Evaluate side-chains 343 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 285 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 315 MET Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 442 VAL 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 717 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 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 J residue 81 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 862 THR 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 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 72 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 305 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 283 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 15 optimal weight: 0.0040 chunk 275 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.114803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.087397 restraints weight = 75181.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.090475 restraints weight = 36371.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.091569 restraints weight = 21326.667| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27432 Z= 0.169 Angle : 0.620 11.315 37487 Z= 0.320 Chirality : 0.042 0.219 4317 Planarity : 0.004 0.046 4558 Dihedral : 15.987 173.489 4692 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.70 % Allowed : 22.33 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.15), residues: 3152 helix: 1.33 (0.15), residues: 1146 sheet: 0.45 (0.28), residues: 359 loop : -0.28 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 115 HIS 0.022 0.001 HIS G 23 PHE 0.036 0.002 PHE I1025 TYR 0.048 0.002 TYR I1229 ARG 0.008 0.000 ARG K 69 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 1140) hydrogen bonds : angle 4.66970 ( 3221) covalent geometry : bond 0.00385 (27432) covalent geometry : angle 0.62042 (37487) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8781.77 seconds wall clock time: 154 minutes 29.79 seconds (9269.79 seconds total)