Starting phenix.real_space_refine on Mon Aug 25 09:48:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g2w_29683/08_2025/8g2w_29683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g2w_29683/08_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_29683/08_2025/8g2w_29683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g2w_29683/08_2025/8g2w_29683.map" model { file = "/net/cci-nas-00/data/ceres_data/8g2w_29683/08_2025/8g2w_29683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g2w_29683/08_2025/8g2w_29683.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 94 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16495 2.51 5 N 4755 2.21 5 O 5378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26829 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 388 Inner-chain residues flagged as termini: ['pdbres=" DG A 25 "'] Classifications: {'DNA': 19} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 18} Chain: "B" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 631 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "G" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1708 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 1 Chain: "H" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1693 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10381 Classifications: {'peptide': 1316} Link IDs: {'PTRANS': 55, 'TRANS': 1260} Chain breaks: 1 Chain: "J" Number of atoms: 10403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10403 Classifications: {'peptide': 1337} Link IDs: {'PTRANS': 55, 'TRANS': 1281} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 997 Classifications: {'RNA': 47} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 11, 'rna3p': 35} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.45, per 1000 atoms: 0.20 Number of scatterers: 26829 At special positions: 0 Unit cell: (135, 157, 161, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 106 16.00 P 94 15.00 Mg 1 11.99 O 5378 8.00 N 4755 7.00 C 16495 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 866.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 41 sheets defined 39.4% alpha, 15.6% beta 32 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 Processing helix chain 'G' and resid 77 through 88 Processing helix chain 'G' and resid 212 through 232 removed outlier: 3.607A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.642A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 212 through 228 Processing helix chain 'H' and resid 228 through 233 removed outlier: 3.545A pdb=" N VAL H 232 " --> pdb=" O LEU H 228 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP H 233 " --> pdb=" O GLU H 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 228 through 233' Processing helix chain 'I' and resid 4 through 10 Processing helix chain 'I' and resid 28 through 40 Processing helix chain 'I' and resid 48 through 56 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.202A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 4.028A pdb=" N LEU I 246 " --> pdb=" O VAL I 242 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG I 247 " --> pdb=" O PRO I 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 242 through 247' Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 295 removed outlier: 3.833A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 329 Processing helix chain 'I' and resid 345 through 354 removed outlier: 3.578A pdb=" N GLU I 349 " --> pdb=" O PRO I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 482 Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.597A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 529 Processing helix chain 'I' and resid 544 through 549 removed outlier: 3.550A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 608 through 614 removed outlier: 3.743A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 614' Processing helix chain 'I' and resid 662 through 667 removed outlier: 3.553A pdb=" N LEU I 667 " --> pdb=" O VAL I 663 " (cutoff:3.500A) Processing helix chain 'I' and resid 675 through 688 removed outlier: 3.758A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 865 removed outlier: 3.775A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU I 865 " --> pdb=" O ALA I 861 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 977 Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.611A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS I 991 " --> pdb=" O GLU I 987 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 3.866A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1151 Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.536A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 removed outlier: 3.615A pdb=" N LYS I1242 " --> pdb=" O LEU I1238 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1333 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 95 through 101 removed outlier: 3.762A pdb=" N ARG J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU J 100 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 119 removed outlier: 3.554A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 162 through 172 Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 255 through 259 Processing helix chain 'J' and resid 264 through 286 removed outlier: 3.830A pdb=" N LEU J 268 " --> pdb=" O ASP J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 318 through 322 removed outlier: 3.535A pdb=" N LYS J 321 " --> pdb=" O GLY J 318 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG J 322 " --> pdb=" O SER J 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 318 through 322' Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 418 removed outlier: 3.720A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 458 removed outlier: 4.037A pdb=" N ALA J 455 " --> pdb=" O PRO J 451 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA J 456 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 540 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.881A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 594 removed outlier: 3.851A pdb=" N GLN J 594 " --> pdb=" O SER J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 613 through 636 Processing helix chain 'J' and resid 647 through 670 removed outlier: 4.426A pdb=" N HIS J 651 " --> pdb=" O PRO J 647 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.612A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 895 through 900 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.619A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1068 through 1074 removed outlier: 4.355A pdb=" N LEU J1074 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 removed outlier: 3.599A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 4.036A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 3.981A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.735A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 Processing helix chain 'J' and resid 1361 through 1373 removed outlier: 4.074A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 33 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 80 removed outlier: 3.514A pdb=" N GLU K 79 " --> pdb=" O GLN K 75 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 17 removed outlier: 4.005A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 115 through 116 removed outlier: 3.830A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.556A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 15 through 18 removed outlier: 4.611A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR H 27 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU H 198 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA H 189 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS H 200 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL H 187 " --> pdb=" O LYS H 200 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL H 202 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 99 through 105 removed outlier: 3.699A pdb=" N LEU H 102 " --> pdb=" O MET H 142 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.967A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.359A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 66 through 75 removed outlier: 3.757A pdb=" N VAL I 71 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.414A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB8, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.703A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.917A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.541A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.612A pdb=" N ASP I 654 " --> pdb=" O ALA I 617 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE I 616 " --> pdb=" O ARG I 637 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 717 removed outlier: 7.128A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 750 through 752 removed outlier: 6.916A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN I 725 " --> pdb=" O VAL I 733 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 3.580A pdb=" N VAL I1225 " --> pdb=" O ILE I1210 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.717A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.717A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.991A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD3, first strand: chain 'I' and resid 1335 through 1338 Processing sheet with id=AD4, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.626A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.056A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 143 through 145 Processing sheet with id=AD6, first strand: chain 'J' and resid 350 through 356 removed outlier: 7.412A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER J 353 " --> pdb=" O MET J 466 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 547 through 556 Processing sheet with id=AD8, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD9, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.953A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.505A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 1024 through 1025 removed outlier: 3.506A pdb=" N ILE J1124 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE J1106 " --> pdb=" O ARG J1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id=AE4, first strand: chain 'J' and resid 1186 through 1190 removed outlier: 4.325A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE J1177 " --> pdb=" O TYR J1186 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1279 through 1281 1072 hydrogen bonds defined for protein. 3063 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 6.75 Time building geometry restraints manager: 2.24 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 25.580 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.560 ------------------------------------------------------------------------------- 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 : 14.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.38 % Favored : 97.59 % Rotamer: Outliers : 0.11 % Allowed : 0.37 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.15), residues: 3152 helix: 1.84 (0.15), residues: 1105 sheet: 1.00 (0.25), residues: 425 loop : 0.28 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 779 TYR 0.015 0.001 TYR J 631 PHE 0.018 0.001 PHE J 461 TRP 0.008 0.001 TRP I 183 HIS 0.007 0.001 HIS J1366 Details of bonding type rmsd covalent geometry : bond 0.00367 (27432) covalent geometry : angle 0.63293 (37487) hydrogen bonds : bond 0.17679 ( 1140) hydrogen bonds : angle 7.10663 ( 3221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 704 time to evaluate : 0.938 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: 0.1917 time to fit residues: 203.9553 Evaluate side-chains 341 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.0170 chunk 298 optimal weight: 6.9990 overall best weight: 2.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 HIS G 41 ASN H 194 GLN I 46 GLN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 450 ASN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 684 ASN I 799 ASN I 808 ASN I 811 ASN ** I 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1209 GLN I1244 HIS I1264 GLN ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1195 GLN J1197 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.116302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.087772 restraints weight = 74406.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.090542 restraints weight = 35125.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.092359 restraints weight = 22143.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.093457 restraints weight = 16843.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.093891 restraints weight = 14401.505| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27432 Z= 0.197 Angle : 0.653 13.060 37487 Z= 0.343 Chirality : 0.043 0.268 4317 Planarity : 0.005 0.056 4558 Dihedral : 15.908 177.336 4692 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.30 % Allowed : 13.62 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.14), residues: 3152 helix: 1.57 (0.15), residues: 1139 sheet: 0.95 (0.26), residues: 397 loop : 0.14 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG J 978 TYR 0.032 0.002 TYR I1229 PHE 0.019 0.002 PHE J 377 TRP 0.011 0.002 TRP J 580 HIS 0.013 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00444 (27432) covalent geometry : angle 0.65335 (37487) hydrogen bonds : bond 0.04699 ( 1140) hydrogen bonds : angle 5.34081 ( 3221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 394 time to evaluate : 1.062 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 178 SER cc_start: 0.8269 (t) cc_final: 0.8050 (p) REVERT: H 32 GLU cc_start: 0.7313 (tp30) cc_final: 0.7033 (mm-30) REVERT: H 185 TYR cc_start: 0.8914 (p90) cc_final: 0.8605 (p90) REVERT: I 116 ASP cc_start: 0.6550 (p0) cc_final: 0.6239 (t70) REVERT: I 142 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7636 (mt-10) REVERT: I 414 ILE cc_start: 0.9165 (mm) cc_final: 0.8641 (tp) REVERT: I 422 LYS cc_start: 0.7168 (mptt) cc_final: 0.6861 (mptt) REVERT: I 516 ASP cc_start: 0.7369 (p0) cc_final: 0.6509 (p0) REVERT: I 788 SER cc_start: 0.9171 (m) cc_final: 0.8806 (p) REVERT: I 798 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7106 (mm-40) REVERT: I 1085 MET cc_start: 0.9128 (mmm) cc_final: 0.8678 (mmm) REVERT: I 1273 MET cc_start: 0.8453 (mtp) cc_final: 0.8036 (mtt) REVERT: J 96 LYS cc_start: 0.8223 (ttmt) cc_final: 0.7900 (mtpt) REVERT: J 97 VAL cc_start: 0.7638 (t) cc_final: 0.7013 (t) REVERT: J 100 GLU cc_start: 0.8214 (mp0) cc_final: 0.7636 (mp0) REVERT: J 137 ARG cc_start: 0.8525 (mtp-110) cc_final: 0.8020 (ptp90) REVERT: J 301 GLU cc_start: 0.8547 (tp30) cc_final: 0.8305 (tm-30) REVERT: J 418 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7055 (mm-30) REVERT: J 466 MET cc_start: 0.8068 (mtm) cc_final: 0.7865 (mtt) REVERT: J 532 GLU cc_start: 0.8155 (tt0) cc_final: 0.7924 (tt0) REVERT: J 656 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7648 (mt-10) REVERT: J 723 TYR cc_start: 0.8876 (t80) cc_final: 0.8630 (t80) REVERT: J 835 LEU cc_start: 0.8375 (tp) cc_final: 0.8120 (tp) REVERT: J 1025 MET cc_start: 0.8520 (mpp) cc_final: 0.8267 (mpp) REVERT: J 1123 ARG cc_start: 0.8301 (mtt180) cc_final: 0.7986 (mtp180) REVERT: J 1254 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8017 (mt-10) REVERT: K 43 ASN cc_start: 0.9030 (t0) cc_final: 0.8742 (t0) outliers start: 62 outliers final: 37 residues processed: 434 average time/residue: 0.1711 time to fit residues: 118.3890 Evaluate side-chains 347 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 310 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 692 THR Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 835 GLU Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 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 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 978 ARG Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 258 optimal weight: 0.9980 chunk 301 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 221 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 490 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 628 HIS I 766 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1209 GLN I1244 HIS I1256 GLN ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1010 GLN J1235 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.108706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.080799 restraints weight = 71651.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.083194 restraints weight = 37228.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.084801 restraints weight = 24377.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.085801 restraints weight = 18682.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.086369 restraints weight = 16010.475| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27432 Z= 0.171 Angle : 0.609 13.059 37487 Z= 0.319 Chirality : 0.042 0.253 4317 Planarity : 0.004 0.056 4558 Dihedral : 15.900 177.207 4692 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.00 % Allowed : 15.70 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.14), residues: 3152 helix: 1.44 (0.15), residues: 1140 sheet: 0.72 (0.26), residues: 387 loop : 0.03 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 978 TYR 0.025 0.002 TYR H 177 PHE 0.028 0.002 PHE I1025 TRP 0.011 0.002 TRP I1276 HIS 0.014 0.001 HIS I1244 Details of bonding type rmsd covalent geometry : bond 0.00381 (27432) covalent geometry : angle 0.60935 (37487) hydrogen bonds : bond 0.04283 ( 1140) hydrogen bonds : angle 5.09397 ( 3221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 350 time to evaluate : 0.754 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: 0.8754 (t0) cc_final: 0.8287 (t0) REVERT: G 178 SER cc_start: 0.8312 (t) cc_final: 0.8090 (p) REVERT: G 185 TYR cc_start: 0.8714 (p90) cc_final: 0.8467 (p90) REVERT: H 185 TYR cc_start: 0.8898 (p90) cc_final: 0.8604 (p90) REVERT: I 116 ASP cc_start: 0.6182 (p0) cc_final: 0.5869 (t70) REVERT: I 142 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7517 (mt-10) REVERT: I 239 MET cc_start: 0.4186 (tmm) cc_final: 0.3892 (tmm) REVERT: I 422 LYS cc_start: 0.7200 (mptt) cc_final: 0.6592 (mptt) REVERT: I 516 ASP cc_start: 0.7034 (p0) cc_final: 0.6441 (p0) REVERT: I 785 ASP cc_start: 0.6682 (m-30) cc_final: 0.6385 (p0) REVERT: I 788 SER cc_start: 0.9105 (m) cc_final: 0.8705 (p) REVERT: I 798 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7146 (mm-40) REVERT: I 1040 ASP cc_start: 0.6554 (t70) cc_final: 0.6335 (t70) REVERT: I 1041 ASP cc_start: 0.8378 (p0) cc_final: 0.8134 (p0) REVERT: I 1085 MET cc_start: 0.9044 (mmm) cc_final: 0.8591 (mmm) REVERT: I 1273 MET cc_start: 0.8312 (mtp) cc_final: 0.7936 (mtt) REVERT: J 96 LYS cc_start: 0.8300 (ttmt) cc_final: 0.7901 (mtpt) REVERT: J 97 VAL cc_start: 0.7583 (t) cc_final: 0.7196 (t) REVERT: J 100 GLU cc_start: 0.8158 (mp0) cc_final: 0.7637 (mp0) REVERT: J 137 ARG cc_start: 0.8422 (mtp-110) cc_final: 0.8055 (ptp90) REVERT: J 301 GLU cc_start: 0.8466 (tp30) cc_final: 0.8233 (tm-30) REVERT: J 504 GLN cc_start: 0.7733 (mp10) cc_final: 0.7330 (mp10) REVERT: J 532 GLU cc_start: 0.8042 (tt0) cc_final: 0.7842 (tt0) REVERT: J 644 MET cc_start: 0.7932 (mtm) cc_final: 0.7728 (mtm) REVERT: J 697 MET cc_start: 0.8147 (ttp) cc_final: 0.7893 (ttp) REVERT: J 799 ARG cc_start: 0.8891 (mtm110) cc_final: 0.8234 (mtm110) REVERT: J 1025 MET cc_start: 0.8451 (mpp) cc_final: 0.8211 (mpp) REVERT: J 1123 ARG cc_start: 0.8301 (mtt180) cc_final: 0.7972 (mtp-110) REVERT: J 1254 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7881 (mt-10) REVERT: K 43 ASN cc_start: 0.9050 (t0) cc_final: 0.8796 (t0) outliers start: 81 outliers final: 49 residues processed: 406 average time/residue: 0.1527 time to fit residues: 100.1773 Evaluate side-chains 347 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 298 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 202 VAL 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 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 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 925 SER 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 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 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 262 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 978 ARG Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 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 305 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 150 HIS I 165 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1061 GLN ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS ** I1257 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.109075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.081274 restraints weight = 70994.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.083669 restraints weight = 36822.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.085280 restraints weight = 24148.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.086209 restraints weight = 18506.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.086862 restraints weight = 15894.114| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27432 Z= 0.143 Angle : 0.582 13.959 37487 Z= 0.303 Chirality : 0.041 0.261 4317 Planarity : 0.004 0.055 4558 Dihedral : 15.886 175.292 4692 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.26 % Allowed : 17.22 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.15), residues: 3152 helix: 1.44 (0.15), residues: 1143 sheet: 0.69 (0.26), residues: 397 loop : -0.02 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 978 TYR 0.033 0.002 TYR I1229 PHE 0.028 0.001 PHE I1025 TRP 0.010 0.001 TRP J 580 HIS 0.013 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00322 (27432) covalent geometry : angle 0.58182 (37487) hydrogen bonds : bond 0.03986 ( 1140) hydrogen bonds : angle 4.87904 ( 3221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 353 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.8158 (m-80) cc_final: 0.7580 (t80) REVERT: G 137 ASN cc_start: 0.8745 (t0) cc_final: 0.8377 (t0) REVERT: H 48 LEU cc_start: 0.9221 (mt) cc_final: 0.9003 (mt) REVERT: H 185 TYR cc_start: 0.8876 (p90) cc_final: 0.8560 (p90) REVERT: H 227 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7362 (mm-40) REVERT: I 116 ASP cc_start: 0.6298 (p0) cc_final: 0.6066 (t70) REVERT: I 142 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7657 (mt-10) REVERT: I 422 LYS cc_start: 0.7249 (mptt) cc_final: 0.6857 (mptt) REVERT: I 516 ASP cc_start: 0.7043 (p0) cc_final: 0.6415 (p0) REVERT: I 785 ASP cc_start: 0.6753 (m-30) cc_final: 0.6467 (p0) REVERT: I 788 SER cc_start: 0.9091 (m) cc_final: 0.8681 (p) REVERT: I 798 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7142 (mm-40) REVERT: I 1040 ASP cc_start: 0.6535 (t70) cc_final: 0.6277 (t70) REVERT: I 1041 ASP cc_start: 0.8287 (p0) cc_final: 0.8074 (p0) REVERT: I 1085 MET cc_start: 0.9033 (mmm) cc_final: 0.8576 (mmm) REVERT: I 1273 MET cc_start: 0.8221 (mtp) cc_final: 0.7861 (mtt) REVERT: J 96 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7834 (mtpt) REVERT: J 97 VAL cc_start: 0.7508 (t) cc_final: 0.7167 (t) REVERT: J 100 GLU cc_start: 0.8157 (mp0) cc_final: 0.7649 (mp0) REVERT: J 137 ARG cc_start: 0.8518 (mtp-110) cc_final: 0.8131 (ptp90) REVERT: J 301 GLU cc_start: 0.8687 (tp30) cc_final: 0.8298 (tm-30) REVERT: J 356 THR cc_start: 0.8694 (m) cc_final: 0.8486 (m) REVERT: J 398 LYS cc_start: 0.8267 (mttt) cc_final: 0.7963 (mtmm) REVERT: J 504 GLN cc_start: 0.7763 (mp10) cc_final: 0.7344 (mp10) REVERT: J 532 GLU cc_start: 0.8043 (tt0) cc_final: 0.7799 (tt0) REVERT: J 1025 MET cc_start: 0.8483 (mpp) cc_final: 0.8224 (mpp) REVERT: J 1123 ARG cc_start: 0.8346 (mtt180) cc_final: 0.8065 (mmm160) REVERT: J 1254 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7867 (mt-10) REVERT: K 43 ASN cc_start: 0.9057 (t0) cc_final: 0.8819 (t0) REVERT: K 65 ASP cc_start: 0.8196 (m-30) cc_final: 0.7993 (m-30) outliers start: 88 outliers final: 61 residues processed: 412 average time/residue: 0.1652 time to fit residues: 108.5225 Evaluate side-chains 368 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 307 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain 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 531 SER 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 692 THR 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 925 SER Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1122 LYS Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 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 133 ARG 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 434 ILE Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 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 302 optimal weight: 0.9980 chunk 201 optimal weight: 0.0970 chunk 239 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 477 GLN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1197 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.107423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.079759 restraints weight = 71481.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.082092 restraints weight = 37314.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.083635 restraints weight = 24526.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.084631 restraints weight = 18855.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.085164 restraints weight = 16147.216| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27432 Z= 0.181 Angle : 0.607 13.467 37487 Z= 0.314 Chirality : 0.042 0.215 4317 Planarity : 0.004 0.053 4558 Dihedral : 15.907 175.309 4692 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.78 % Allowed : 18.55 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.15), residues: 3152 helix: 1.41 (0.15), residues: 1152 sheet: 0.57 (0.26), residues: 399 loop : -0.07 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 744 TYR 0.030 0.002 TYR H 177 PHE 0.038 0.002 PHE I1025 TRP 0.017 0.002 TRP I1276 HIS 0.013 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00407 (27432) covalent geometry : angle 0.60650 (37487) hydrogen bonds : bond 0.04039 ( 1140) hydrogen bonds : angle 4.85119 ( 3221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 310 time to evaluate : 1.100 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 137 ASN cc_start: 0.8791 (t0) cc_final: 0.8280 (t0) REVERT: G 185 TYR cc_start: 0.8805 (p90) cc_final: 0.8521 (p90) REVERT: H 185 TYR cc_start: 0.8932 (p90) cc_final: 0.8667 (p90) REVERT: I 116 ASP cc_start: 0.6295 (p0) cc_final: 0.6030 (t70) REVERT: I 142 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7698 (mt-10) REVERT: I 516 ASP cc_start: 0.7035 (p0) cc_final: 0.6441 (p0) REVERT: I 788 SER cc_start: 0.9154 (m) cc_final: 0.8758 (p) REVERT: I 798 GLN cc_start: 0.7631 (mm-40) cc_final: 0.7183 (mm-40) REVERT: I 1040 ASP cc_start: 0.6584 (t70) cc_final: 0.6242 (t0) REVERT: I 1041 ASP cc_start: 0.8391 (p0) cc_final: 0.7904 (p0) REVERT: I 1085 MET cc_start: 0.9049 (mmm) cc_final: 0.8474 (mmm) REVERT: I 1273 MET cc_start: 0.8395 (mtp) cc_final: 0.8185 (mtp) REVERT: I 1329 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7142 (mt-10) REVERT: J 96 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7985 (mttt) REVERT: J 97 VAL cc_start: 0.7539 (t) cc_final: 0.7212 (t) REVERT: J 100 GLU cc_start: 0.8084 (mp0) cc_final: 0.7647 (mp0) REVERT: J 137 ARG cc_start: 0.8481 (mtp-110) cc_final: 0.8127 (ptp90) REVERT: J 281 ARG cc_start: 0.8285 (tmm-80) cc_final: 0.7948 (tmm-80) REVERT: J 301 GLU cc_start: 0.8677 (tp30) cc_final: 0.8351 (tm-30) REVERT: J 356 THR cc_start: 0.8777 (m) cc_final: 0.8569 (m) REVERT: J 375 GLU cc_start: 0.7832 (mp0) cc_final: 0.7429 (mp0) REVERT: J 504 GLN cc_start: 0.7828 (mp10) cc_final: 0.7389 (mp10) REVERT: J 697 MET cc_start: 0.8020 (ttp) cc_final: 0.7733 (ttp) REVERT: J 1025 MET cc_start: 0.8478 (mpp) cc_final: 0.8232 (mpp) REVERT: J 1123 ARG cc_start: 0.8347 (mtt180) cc_final: 0.8077 (mtp180) REVERT: J 1189 MET cc_start: 0.7813 (mmt) cc_final: 0.7275 (tpt) REVERT: J 1254 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7886 (mt-10) outliers start: 102 outliers final: 69 residues processed: 386 average time/residue: 0.1621 time to fit residues: 101.3773 Evaluate side-chains 357 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 288 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 G residue 177 TYR 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 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 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 800 MET Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 925 SER 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 I residue 1303 LYS 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 199 GLU 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 434 ILE Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 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 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 Chi-restraints excluded: chain K residue 62 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 57 optimal weight: 20.0000 chunk 219 optimal weight: 0.8980 chunk 280 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 304 optimal weight: 6.9990 chunk 316 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 234 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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** ** 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 = 0.3754 r_free = 0.3754 target = 0.108641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.081320 restraints weight = 71417.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.083688 restraints weight = 36989.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.085254 restraints weight = 24181.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.086205 restraints weight = 18538.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.086661 restraints weight = 15909.258| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27432 Z= 0.158 Angle : 0.592 13.586 37487 Z= 0.305 Chirality : 0.041 0.214 4317 Planarity : 0.004 0.051 4558 Dihedral : 15.946 174.536 4692 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.37 % Allowed : 19.36 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.15), residues: 3152 helix: 1.45 (0.15), residues: 1138 sheet: 0.53 (0.27), residues: 378 loop : -0.08 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 69 TYR 0.029 0.002 TYR I1229 PHE 0.024 0.001 PHE I1025 TRP 0.013 0.001 TRP J 580 HIS 0.004 0.001 HIS J1366 Details of bonding type rmsd covalent geometry : bond 0.00358 (27432) covalent geometry : angle 0.59199 (37487) hydrogen bonds : bond 0.03933 ( 1140) hydrogen bonds : angle 4.79077 ( 3221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 314 time to evaluate : 1.075 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: 0.8402 (m-80) cc_final: 0.7743 (t80) REVERT: G 137 ASN cc_start: 0.8696 (t0) cc_final: 0.8195 (t0) REVERT: G 185 TYR cc_start: 0.8790 (p90) cc_final: 0.8524 (p90) REVERT: H 104 LYS cc_start: 0.7256 (mmmt) cc_final: 0.6905 (tttt) REVERT: H 185 TYR cc_start: 0.8941 (p90) cc_final: 0.8672 (p90) REVERT: I 47 TYR cc_start: 0.4873 (m-80) cc_final: 0.4650 (m-10) REVERT: I 116 ASP cc_start: 0.6162 (p0) cc_final: 0.5914 (t70) REVERT: I 516 ASP cc_start: 0.6983 (p0) cc_final: 0.6420 (p0) REVERT: I 517 GLN cc_start: 0.7825 (tt0) cc_final: 0.7556 (tt0) REVERT: I 788 SER cc_start: 0.9088 (m) cc_final: 0.8794 (p) REVERT: I 798 GLN cc_start: 0.7410 (mm-40) cc_final: 0.7208 (mm-40) REVERT: I 1040 ASP cc_start: 0.6526 (t70) cc_final: 0.6218 (t0) REVERT: I 1041 ASP cc_start: 0.8276 (p0) cc_final: 0.7934 (p0) REVERT: I 1085 MET cc_start: 0.9020 (mmm) cc_final: 0.8492 (mmm) REVERT: I 1272 GLU cc_start: 0.7613 (tp30) cc_final: 0.7370 (tp30) REVERT: I 1273 MET cc_start: 0.8335 (mtp) cc_final: 0.8115 (mtp) REVERT: I 1329 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7331 (mt-10) REVERT: J 96 LYS cc_start: 0.8298 (ttmt) cc_final: 0.7954 (mttt) REVERT: J 97 VAL cc_start: 0.7563 (t) cc_final: 0.7207 (t) REVERT: J 100 GLU cc_start: 0.8031 (mp0) cc_final: 0.7611 (mp0) REVERT: J 137 ARG cc_start: 0.8407 (mtp-110) cc_final: 0.8148 (ptp90) REVERT: J 281 ARG cc_start: 0.8286 (tmm-80) cc_final: 0.7930 (tmm-80) REVERT: J 301 GLU cc_start: 0.8669 (tp30) cc_final: 0.8389 (tm-30) REVERT: J 330 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7889 (ttp) REVERT: J 370 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8576 (mttm) REVERT: J 375 GLU cc_start: 0.7743 (mp0) cc_final: 0.7335 (mp0) REVERT: J 382 TYR cc_start: 0.9128 (m-80) cc_final: 0.8902 (m-80) REVERT: J 504 GLN cc_start: 0.7785 (mp10) cc_final: 0.7324 (mp10) REVERT: J 697 MET cc_start: 0.8082 (ttp) cc_final: 0.7851 (ttp) REVERT: J 1025 MET cc_start: 0.8498 (mpp) cc_final: 0.8227 (mpp) REVERT: J 1123 ARG cc_start: 0.8328 (mtt180) cc_final: 0.8082 (mtp180) REVERT: J 1155 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8642 (mp) REVERT: J 1254 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7877 (mt-10) REVERT: J 1370 MET cc_start: 0.7476 (mmp) cc_final: 0.6939 (mmt) outliers start: 91 outliers final: 73 residues processed: 378 average time/residue: 0.1503 time to fit residues: 91.5535 Evaluate side-chains 371 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 295 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 G residue 177 TYR 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 221 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 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 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 925 SER 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 1259 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 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 107 LEU Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 434 ILE 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 541 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 4 optimal weight: 6.9990 chunk 305 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 217 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 227 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 41 ASN I 165 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1072 ASN ** 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 = 0.3895 r_free = 0.3895 target = 0.112476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.083873 restraints weight = 74314.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.086542 restraints weight = 35787.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.088282 restraints weight = 22780.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.089328 restraints weight = 17419.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.089844 restraints weight = 14952.190| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 27432 Z= 0.255 Angle : 0.660 12.701 37487 Z= 0.343 Chirality : 0.043 0.225 4317 Planarity : 0.004 0.051 4558 Dihedral : 16.070 174.596 4692 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.96 % Allowed : 19.66 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.15), residues: 3152 helix: 1.23 (0.15), residues: 1155 sheet: 0.35 (0.27), residues: 375 loop : -0.22 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I1246 TYR 0.035 0.002 TYR I1229 PHE 0.024 0.002 PHE I1025 TRP 0.014 0.002 TRP J 115 HIS 0.012 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00570 (27432) covalent geometry : angle 0.65993 (37487) hydrogen bonds : bond 0.04278 ( 1140) hydrogen bonds : angle 4.95979 ( 3221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 306 time to evaluate : 1.106 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: 0.8606 (m-80) cc_final: 0.7894 (t80) REVERT: G 137 ASN cc_start: 0.9074 (t0) cc_final: 0.8652 (t0) REVERT: G 174 ASP cc_start: 0.7896 (p0) cc_final: 0.7685 (p0) REVERT: G 185 TYR cc_start: 0.8912 (p90) cc_final: 0.8675 (p90) REVERT: H 185 TYR cc_start: 0.9104 (p90) cc_final: 0.8819 (p90) REVERT: I 116 ASP cc_start: 0.6830 (p0) cc_final: 0.6473 (t70) REVERT: I 414 ILE cc_start: 0.9139 (mm) cc_final: 0.8671 (tp) REVERT: I 422 LYS cc_start: 0.7432 (mptt) cc_final: 0.6685 (tptt) REVERT: I 516 ASP cc_start: 0.7357 (p0) cc_final: 0.6845 (p0) REVERT: I 517 GLN cc_start: 0.8266 (tt0) cc_final: 0.7876 (tt0) REVERT: I 788 SER cc_start: 0.9208 (m) cc_final: 0.8953 (p) REVERT: I 798 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7294 (mm-40) REVERT: I 1040 ASP cc_start: 0.7112 (t70) cc_final: 0.6850 (t70) REVERT: I 1085 MET cc_start: 0.9179 (mmm) cc_final: 0.8729 (mmm) REVERT: I 1272 GLU cc_start: 0.7639 (tp30) cc_final: 0.7399 (tp30) REVERT: I 1273 MET cc_start: 0.8716 (mtp) cc_final: 0.8366 (mtp) REVERT: I 1329 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7451 (mt-10) REVERT: J 96 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8146 (mttt) REVERT: J 97 VAL cc_start: 0.7532 (t) cc_final: 0.6898 (t) REVERT: J 100 GLU cc_start: 0.8233 (mp0) cc_final: 0.7623 (mp0) REVERT: J 137 ARG cc_start: 0.8538 (mtp-110) cc_final: 0.8089 (ptp90) REVERT: J 140 TYR cc_start: 0.8185 (m-10) cc_final: 0.7856 (m-10) REVERT: J 281 ARG cc_start: 0.8567 (tmm-80) cc_final: 0.8021 (tmm-80) REVERT: J 301 GLU cc_start: 0.8754 (tp30) cc_final: 0.8402 (tm-30) REVERT: J 330 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7874 (ttp) REVERT: J 375 GLU cc_start: 0.8135 (mp0) cc_final: 0.7616 (mp0) REVERT: J 382 TYR cc_start: 0.9281 (m-80) cc_final: 0.9010 (m-80) REVERT: J 398 LYS cc_start: 0.8328 (mptt) cc_final: 0.8080 (mppt) REVERT: J 504 GLN cc_start: 0.7874 (mp10) cc_final: 0.7445 (mp10) REVERT: J 799 ARG cc_start: 0.9001 (mtm110) cc_final: 0.7994 (mtm110) REVERT: J 1025 MET cc_start: 0.8679 (mpp) cc_final: 0.8344 (mpp) REVERT: J 1123 ARG cc_start: 0.8464 (mtt180) cc_final: 0.8072 (mtp180) REVERT: J 1155 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8580 (mp) outliers start: 107 outliers final: 88 residues processed: 382 average time/residue: 0.1818 time to fit residues: 112.2372 Evaluate side-chains 375 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 285 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 152 TYR Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR 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 124 MET 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 369 MET 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 603 ILE 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 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 925 SER Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 434 ILE 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 573 THR Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 918 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 270 optimal weight: 0.8980 chunk 178 optimal weight: 6.9990 chunk 96 optimal weight: 0.0370 chunk 230 optimal weight: 6.9990 chunk 295 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 292 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 overall best weight: 2.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 ASN ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.105744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.078399 restraints weight = 71153.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.080680 restraints weight = 37286.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.082121 restraints weight = 24540.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.083137 restraints weight = 18997.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.083566 restraints weight = 16159.593| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27432 Z= 0.199 Angle : 0.629 12.926 37487 Z= 0.325 Chirality : 0.043 0.394 4317 Planarity : 0.004 0.053 4558 Dihedral : 16.125 173.601 4692 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.70 % Allowed : 20.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.15), residues: 3152 helix: 1.22 (0.15), residues: 1148 sheet: 0.28 (0.28), residues: 375 loop : -0.26 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J1372 TYR 0.028 0.002 TYR I1229 PHE 0.045 0.002 PHE I1025 TRP 0.013 0.002 TRP J 580 HIS 0.014 0.001 HIS J1366 Details of bonding type rmsd covalent geometry : bond 0.00450 (27432) covalent geometry : angle 0.62852 (37487) hydrogen bonds : bond 0.04062 ( 1140) hydrogen bonds : angle 4.89235 ( 3221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 304 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.8431 (m-80) cc_final: 0.7735 (t80) REVERT: G 137 ASN cc_start: 0.8774 (t0) cc_final: 0.8351 (t0) REVERT: G 185 TYR cc_start: 0.8804 (p90) cc_final: 0.8523 (p90) REVERT: H 185 TYR cc_start: 0.9050 (p90) cc_final: 0.8773 (p90) REVERT: I 116 ASP cc_start: 0.6331 (p0) cc_final: 0.5976 (t70) REVERT: I 213 LEU cc_start: 0.8724 (mt) cc_final: 0.8033 (mt) REVERT: I 414 ILE cc_start: 0.9084 (mm) cc_final: 0.8703 (tp) REVERT: I 422 LYS cc_start: 0.7492 (mptt) cc_final: 0.6315 (tptt) REVERT: I 510 GLN cc_start: 0.8406 (tt0) cc_final: 0.8123 (tp40) REVERT: I 516 ASP cc_start: 0.7122 (p0) cc_final: 0.6593 (p0) REVERT: I 517 GLN cc_start: 0.8047 (tt0) cc_final: 0.7652 (tt0) REVERT: I 601 ASP cc_start: 0.8538 (t0) cc_final: 0.8060 (p0) REVERT: I 788 SER cc_start: 0.9195 (m) cc_final: 0.8963 (p) REVERT: I 798 GLN cc_start: 0.7583 (mm-40) cc_final: 0.7296 (mm-40) REVERT: I 1085 MET cc_start: 0.9027 (mmm) cc_final: 0.8469 (mmm) REVERT: I 1273 MET cc_start: 0.8473 (mtp) cc_final: 0.8176 (mtp) REVERT: I 1329 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7239 (mt-10) REVERT: J 96 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8190 (mttt) REVERT: J 97 VAL cc_start: 0.7639 (t) cc_final: 0.7009 (t) REVERT: J 100 GLU cc_start: 0.8093 (mp0) cc_final: 0.7607 (mp0) REVERT: J 136 GLU cc_start: 0.8325 (tp30) cc_final: 0.7662 (tp30) REVERT: J 137 ARG cc_start: 0.8405 (mtp-110) cc_final: 0.8120 (ptp90) REVERT: J 249 LEU cc_start: 0.9133 (mt) cc_final: 0.8808 (tt) REVERT: J 281 ARG cc_start: 0.8375 (tmm-80) cc_final: 0.7936 (tmm-80) REVERT: J 330 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7793 (ttp) REVERT: J 375 GLU cc_start: 0.7849 (mp0) cc_final: 0.7396 (mp0) REVERT: J 382 TYR cc_start: 0.9197 (m-10) cc_final: 0.8910 (m-80) REVERT: J 398 LYS cc_start: 0.8397 (mptt) cc_final: 0.8145 (mppt) REVERT: J 504 GLN cc_start: 0.7789 (mp10) cc_final: 0.7364 (mp10) REVERT: J 697 MET cc_start: 0.8153 (ttp) cc_final: 0.7847 (ttp) REVERT: J 821 MET cc_start: 0.8801 (tpp) cc_final: 0.8587 (tpp) REVERT: J 1025 MET cc_start: 0.8593 (mpp) cc_final: 0.8263 (mpp) REVERT: J 1123 ARG cc_start: 0.8258 (mtt180) cc_final: 0.7987 (mtp180) REVERT: J 1155 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8728 (mp) outliers start: 100 outliers final: 83 residues processed: 374 average time/residue: 0.1789 time to fit residues: 108.5618 Evaluate side-chains 373 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 288 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 G residue 177 TYR 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 484 LEU 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 603 ILE 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 717 VAL Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 871 VAL Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 967 LEU Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1170 MET Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1265 PHE Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 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 107 LEU Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 434 ILE 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 573 THR Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 743 MET Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 994 SER Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 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 62 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 117 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 273 optimal weight: 9.9990 chunk 211 optimal weight: 0.6980 chunk 288 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 95 optimal weight: 0.1980 chunk 133 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 165 HIS ** I 799 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.115343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.087313 restraints weight = 74536.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.090111 restraints weight = 35449.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.091872 restraints weight = 22256.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.092957 restraints weight = 16899.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.093562 restraints weight = 14444.607| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27432 Z= 0.137 Angle : 0.607 13.201 37487 Z= 0.312 Chirality : 0.042 0.215 4317 Planarity : 0.004 0.050 4558 Dihedral : 16.094 172.508 4692 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.22 % Allowed : 21.33 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.15), residues: 3152 helix: 1.26 (0.15), residues: 1149 sheet: 0.40 (0.28), residues: 365 loop : -0.26 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 69 TYR 0.025 0.001 TYR I1229 PHE 0.040 0.001 PHE I1025 TRP 0.024 0.002 TRP J 115 HIS 0.009 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00313 (27432) covalent geometry : angle 0.60738 (37487) hydrogen bonds : bond 0.03839 ( 1140) hydrogen bonds : angle 4.72259 ( 3221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 317 time to evaluate : 1.055 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: 0.8492 (m-80) cc_final: 0.7787 (t80) REVERT: G 137 ASN cc_start: 0.9007 (t0) cc_final: 0.8742 (t0) REVERT: G 185 TYR cc_start: 0.8758 (p90) cc_final: 0.8482 (p90) REVERT: H 104 LYS cc_start: 0.7328 (mmmt) cc_final: 0.6931 (tttt) REVERT: H 117 HIS cc_start: 0.7725 (p-80) cc_final: 0.7329 (p90) REVERT: H 125 LYS cc_start: 0.8569 (mmmm) cc_final: 0.8242 (mmmt) REVERT: H 185 TYR cc_start: 0.9045 (p90) cc_final: 0.8831 (p90) REVERT: I 116 ASP cc_start: 0.6931 (p0) cc_final: 0.6574 (t70) REVERT: I 213 LEU cc_start: 0.8779 (mt) cc_final: 0.8155 (mt) REVERT: I 414 ILE cc_start: 0.9118 (mm) cc_final: 0.8660 (tp) REVERT: I 422 LYS cc_start: 0.7408 (mptt) cc_final: 0.6186 (tptt) REVERT: I 516 ASP cc_start: 0.7251 (p0) cc_final: 0.6689 (p0) REVERT: I 601 ASP cc_start: 0.8595 (t0) cc_final: 0.8073 (p0) REVERT: I 788 SER cc_start: 0.9179 (m) cc_final: 0.8791 (p) REVERT: I 798 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7200 (mm-40) REVERT: I 1040 ASP cc_start: 0.6551 (t70) cc_final: 0.5709 (t0) REVERT: I 1041 ASP cc_start: 0.8270 (p0) cc_final: 0.8036 (p0) REVERT: I 1085 MET cc_start: 0.9156 (mmm) cc_final: 0.8643 (mmm) REVERT: I 1119 MET cc_start: 0.8753 (tpp) cc_final: 0.8502 (tpp) REVERT: I 1273 MET cc_start: 0.8538 (mtp) cc_final: 0.8216 (mtp) REVERT: I 1303 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8127 (mtmm) REVERT: I 1329 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7496 (mt-10) REVERT: J 96 LYS cc_start: 0.8291 (ttmt) cc_final: 0.7883 (mttt) REVERT: J 97 VAL cc_start: 0.7436 (t) cc_final: 0.7019 (t) REVERT: J 100 GLU cc_start: 0.8259 (mp0) cc_final: 0.7702 (mp0) REVERT: J 136 GLU cc_start: 0.8514 (tp30) cc_final: 0.8286 (tp30) REVERT: J 137 ARG cc_start: 0.8447 (mtp-110) cc_final: 0.8170 (ptp90) REVERT: J 330 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8047 (ttp) REVERT: J 345 LYS cc_start: 0.8588 (mttm) cc_final: 0.8257 (mttp) REVERT: J 375 GLU cc_start: 0.8132 (mp0) cc_final: 0.7626 (mp0) REVERT: J 382 TYR cc_start: 0.9242 (m-10) cc_final: 0.8881 (m-80) REVERT: J 398 LYS cc_start: 0.8371 (mptt) cc_final: 0.8065 (mppt) REVERT: J 504 GLN cc_start: 0.7749 (mp10) cc_final: 0.7195 (mp10) REVERT: J 532 GLU cc_start: 0.8224 (tt0) cc_final: 0.7875 (tt0) REVERT: J 697 MET cc_start: 0.8289 (ttp) cc_final: 0.8028 (ttp) REVERT: J 821 MET cc_start: 0.8972 (tpp) cc_final: 0.8729 (tpp) REVERT: J 1025 MET cc_start: 0.8627 (mpp) cc_final: 0.8293 (mpp) REVERT: J 1123 ARG cc_start: 0.8374 (mtt180) cc_final: 0.7993 (mtp180) REVERT: J 1155 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8580 (mp) REVERT: J 1370 MET cc_start: 0.7911 (mmp) cc_final: 0.7304 (mmt) outliers start: 87 outliers final: 68 residues processed: 381 average time/residue: 0.1789 time to fit residues: 110.7160 Evaluate side-chains 372 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 301 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 G residue 177 TYR Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 165 HIS Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 531 SER 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 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 925 SER 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 1265 PHE Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 281 optimal weight: 0.3980 chunk 189 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 291 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 292 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 686 GLN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.115869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.088010 restraints weight = 74270.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.090806 restraints weight = 35357.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.092567 restraints weight = 22211.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.093674 restraints weight = 16800.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.094163 restraints weight = 14368.200| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27432 Z= 0.132 Angle : 0.616 13.109 37487 Z= 0.315 Chirality : 0.042 0.215 4317 Planarity : 0.004 0.049 4558 Dihedral : 16.042 172.437 4692 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.78 % Allowed : 22.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.15), residues: 3152 helix: 1.25 (0.15), residues: 1151 sheet: 0.37 (0.28), residues: 376 loop : -0.24 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 69 TYR 0.041 0.002 TYR I1229 PHE 0.037 0.001 PHE I1025 TRP 0.036 0.002 TRP J 115 HIS 0.026 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00300 (27432) covalent geometry : angle 0.61598 (37487) hydrogen bonds : bond 0.03791 ( 1140) hydrogen bonds : angle 4.66940 ( 3221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 323 time to evaluate : 1.074 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: 0.8501 (m-80) cc_final: 0.7740 (t80) REVERT: G 137 ASN cc_start: 0.8984 (t0) cc_final: 0.8771 (t0) REVERT: G 185 TYR cc_start: 0.8719 (p90) cc_final: 0.8437 (p90) REVERT: H 117 HIS cc_start: 0.7650 (p-80) cc_final: 0.7268 (p90) REVERT: H 185 TYR cc_start: 0.9039 (p90) cc_final: 0.8817 (p90) REVERT: I 116 ASP cc_start: 0.7026 (p0) cc_final: 0.6607 (t70) REVERT: I 213 LEU cc_start: 0.8796 (mt) cc_final: 0.8578 (mt) REVERT: I 414 ILE cc_start: 0.9116 (mm) cc_final: 0.8659 (tp) REVERT: I 422 LYS cc_start: 0.7426 (mptt) cc_final: 0.6181 (mptt) REVERT: I 429 MET cc_start: 0.9128 (mmm) cc_final: 0.8819 (mmm) REVERT: I 516 ASP cc_start: 0.7300 (p0) cc_final: 0.6736 (p0) REVERT: I 517 GLN cc_start: 0.8080 (tt0) cc_final: 0.7660 (tt0) REVERT: I 524 ILE cc_start: 0.8954 (tp) cc_final: 0.8705 (tp) REVERT: I 601 ASP cc_start: 0.8624 (t0) cc_final: 0.8082 (p0) REVERT: I 760 ASN cc_start: 0.8251 (m110) cc_final: 0.8047 (t0) REVERT: I 788 SER cc_start: 0.9247 (m) cc_final: 0.8844 (p) REVERT: I 798 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7344 (mm-40) REVERT: I 800 MET cc_start: 0.8770 (pmm) cc_final: 0.8252 (ptp) REVERT: I 1085 MET cc_start: 0.9133 (mmm) cc_final: 0.8660 (mmm) REVERT: I 1119 MET cc_start: 0.8728 (tpp) cc_final: 0.8472 (tpp) REVERT: I 1303 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8178 (mtmm) REVERT: I 1329 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7420 (mt-10) REVERT: J 96 LYS cc_start: 0.8247 (ttmt) cc_final: 0.7856 (mttt) REVERT: J 97 VAL cc_start: 0.7418 (t) cc_final: 0.6948 (t) REVERT: J 100 GLU cc_start: 0.8266 (mp0) cc_final: 0.7689 (mp0) REVERT: J 136 GLU cc_start: 0.8580 (tp30) cc_final: 0.8275 (tp30) REVERT: J 137 ARG cc_start: 0.8396 (mtp-110) cc_final: 0.8156 (ptp90) REVERT: J 330 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7989 (ttp) REVERT: J 345 LYS cc_start: 0.8587 (mttm) cc_final: 0.8265 (mttp) REVERT: J 375 GLU cc_start: 0.8159 (mp0) cc_final: 0.7657 (mp0) REVERT: J 382 TYR cc_start: 0.9231 (m-10) cc_final: 0.8874 (m-80) REVERT: J 398 LYS cc_start: 0.8398 (mptt) cc_final: 0.8081 (mppt) REVERT: J 504 GLN cc_start: 0.7696 (mp10) cc_final: 0.7212 (mp10) REVERT: J 532 GLU cc_start: 0.8263 (tt0) cc_final: 0.7898 (tt0) REVERT: J 697 MET cc_start: 0.8292 (ttp) cc_final: 0.8027 (ttp) REVERT: J 821 MET cc_start: 0.8963 (tpp) cc_final: 0.8738 (tpp) REVERT: J 826 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7967 (mp) REVERT: J 1025 MET cc_start: 0.8644 (mpp) cc_final: 0.8304 (mpp) REVERT: J 1040 MET cc_start: 0.5079 (ptp) cc_final: 0.4673 (pmm) REVERT: J 1123 ARG cc_start: 0.8389 (mtt180) cc_final: 0.7978 (mmm160) REVERT: J 1155 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8576 (mp) REVERT: J 1370 MET cc_start: 0.7975 (mmp) cc_final: 0.7510 (mmt) REVERT: K 69 ARG cc_start: 0.8761 (mtp-110) cc_final: 0.8385 (ttm110) outliers start: 75 outliers final: 67 residues processed: 377 average time/residue: 0.1758 time to fit residues: 108.0161 Evaluate side-chains 370 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 299 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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 H residue 229 GLU 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 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 484 LEU 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 611 GLU Chi-restraints excluded: chain I residue 736 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 925 SER 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 1265 PHE Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1303 LYS Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 370 LYS Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 541 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 826 ILE Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 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 1274 PHE Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain J residue 1353 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 286 optimal weight: 0.0980 chunk 247 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 273 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 127 optimal weight: 0.0770 chunk 9 optimal weight: 0.5980 chunk 183 optimal weight: 0.1980 chunk 271 optimal weight: 9.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 GLN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS J 364 HIS J 690 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.117206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.089756 restraints weight = 74174.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.092542 restraints weight = 34980.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.094325 restraints weight = 21914.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.095416 restraints weight = 16577.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.096063 restraints weight = 14146.722| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27432 Z= 0.122 Angle : 0.611 13.025 37487 Z= 0.312 Chirality : 0.041 0.213 4317 Planarity : 0.004 0.051 4558 Dihedral : 15.981 172.128 4692 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.44 % Allowed : 22.77 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.15), residues: 3152 helix: 1.24 (0.15), residues: 1164 sheet: 0.42 (0.28), residues: 376 loop : -0.27 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 69 TYR 0.031 0.001 TYR I 291 PHE 0.032 0.001 PHE I1025 TRP 0.029 0.002 TRP J 115 HIS 0.004 0.001 HIS I1244 Details of bonding type rmsd covalent geometry : bond 0.00271 (27432) covalent geometry : angle 0.61083 (37487) hydrogen bonds : bond 0.03715 ( 1140) hydrogen bonds : angle 4.61703 ( 3221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4966.04 seconds wall clock time: 86 minutes 41.07 seconds (5201.07 seconds total)