Starting phenix.real_space_refine on Sat Aug 8 08:20:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g1s_29676/08_2026/8g1s_29676.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g1s_29676/08_2026/8g1s_29676.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8g1s_29676/08_2026/8g1s_29676.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g1s_29676/08_2026/8g1s_29676.cif" model { file = "/net/cci-nas-00/data/ceres_data/8g1s_29676/08_2026/8g1s_29676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g1s_29676/08_2026/8g1s_29676.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g1s_29676/08_2026/8g1s_29676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g1s_29676/08_2026/8g1s_29676.map" } 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= 0.057 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 92 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16476 2.51 5 N 4747 2.21 5 O 5366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26788 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 369 Inner-chain residues flagged as termini: ['pdbres=" DG A 26 "'] Classifications: {'DNA': 18} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 17} Chain: "B" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 609 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "G" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1708 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 1 Chain: "H" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1693 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10381 Classifications: {'peptide': 1316} Link IDs: {'PTRANS': 55, 'TRANS': 1260} Chain breaks: 1 Chain: "J" Number of atoms: 10403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10403 Classifications: {'peptide': 1337} Link IDs: {'PTRANS': 55, 'TRANS': 1281} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 997 Classifications: {'RNAv2': 47} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 18, 'rna3p_pyr': 16} Link IDs: {'rna2p': 13, 'rna3p': 33} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.48, per 1000 atoms: 0.20 Number of scatterers: 26788 At special positions: 0 Unit cell: (137, 154, 162, 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 92 15.00 Mg 1 11.99 O 5366 8.00 N 4747 7.00 C 16476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 948.2 milliseconds 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 43 sheets defined 36.7% alpha, 12.1% beta 26 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.601A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'G' and resid 230 through 232 No H-bonds generated for 'chain 'G' and resid 230 through 232' Processing helix chain 'H' and resid 35 through 50 removed outlier: 3.713A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 87 removed outlier: 3.894A pdb=" N LEU H 85 " --> pdb=" O ILE H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'H' and resid 228 through 232 Processing helix chain 'I' and resid 4 through 10 Processing helix chain 'I' and resid 28 through 39 removed outlier: 3.972A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.618A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 246 removed outlier: 3.518A pdb=" N ARG I 245 " --> pdb=" O VAL I 242 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 242 through 246' Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 294 removed outlier: 4.026A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 Processing helix chain 'I' and resid 345 through 354 removed outlier: 4.022A pdb=" N GLU I 349 " --> pdb=" O PRO I 345 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR I 350 " --> pdb=" O TYR I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 437 Processing helix chain 'I' and resid 455 through 479 Processing helix chain 'I' and resid 495 through 507 Processing helix chain 'I' and resid 519 through 526 Processing helix chain 'I' and resid 544 through 549 Processing helix chain 'I' and resid 607 through 614 removed outlier: 4.036A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) Processing helix chain 'I' and resid 662 through 667 Processing helix chain 'I' and resid 675 through 685 Processing helix chain 'I' and resid 704 through 712 removed outlier: 3.773A pdb=" N SER I 712 " --> pdb=" O VAL I 708 " (cutoff:3.500A) Processing helix chain 'I' and resid 819 through 825 removed outlier: 3.987A pdb=" N VAL I 823 " --> pdb=" O SER I 819 " (cutoff:3.500A) Processing helix chain 'I' and resid 858 through 865 removed outlier: 4.288A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU I 865 " --> pdb=" O ALA I 861 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 979 removed outlier: 3.652A pdb=" N ILE I 966 " --> pdb=" O GLU I 962 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU I 967 " --> pdb=" O GLU I 963 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL I 978 " --> pdb=" O ARG I 974 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 990 removed outlier: 4.349A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) Processing helix chain 'I' and resid 1006 through 1038 Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.532A pdb=" N MET I1131 " --> pdb=" O LYS I1127 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.527A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.532A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1280 removed outlier: 3.600A pdb=" N VAL I1275 " --> pdb=" O GLY I1271 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TRP I1276 " --> pdb=" O GLU I1272 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1309 Processing helix chain 'I' and resid 1320 through 1332 Processing helix chain 'J' and resid 28 through 33 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 192 removed outlier: 3.546A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 208 removed outlier: 3.641A pdb=" N GLU J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 229 Processing helix chain 'J' and resid 233 through 238 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 265 through 286 Processing helix chain 'J' and resid 288 through 309 Processing helix chain 'J' and resid 336 through 341 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 403 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.524A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE J 411 " --> pdb=" O VAL J 407 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 434 removed outlier: 3.545A pdb=" N ILE J 434 " --> pdb=" O ARG J 431 " (cutoff:3.500A) Processing helix chain 'J' and resid 453 through 458 removed outlier: 3.561A pdb=" N TYR J 457 " --> pdb=" O VAL J 453 " (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 removed outlier: 3.550A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.616A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 removed outlier: 3.505A pdb=" N GLY J 613 " --> pdb=" O TYR J 609 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.788A pdb=" N ARG J 634 " --> pdb=" O ALA J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 Processing helix chain 'J' and resid 647 through 670 removed outlier: 3.964A pdb=" N HIS J 651 " --> pdb=" O PRO J 647 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.744A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 removed outlier: 3.528A pdb=" N VAL J 839 " --> pdb=" O LEU J 835 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1137 through 1146 Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.769A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 removed outlier: 4.077A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1293 Processing helix chain 'J' and resid 1308 through 1313 Processing helix chain 'J' and resid 1314 through 1316 No H-bonds generated for 'chain 'J' and resid 1314 through 1316' Processing helix chain 'J' and resid 1319 through 1326 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 Processing helix chain 'J' and resid 1362 through 1373 Processing helix chain 'K' and resid 6 through 11 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 78 removed outlier: 3.566A pdb=" N ALA K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 15 Processing sheet with id=AA2, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.519A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 91 removed outlier: 3.668A pdb=" N ARG G 91 " --> pdb=" O GLU G 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 109 Processing sheet with id=AA5, first strand: chain 'G' and resid 180 through 182 removed outlier: 6.571A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 15 through 16 removed outlier: 4.189A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 31 through 32 removed outlier: 3.816A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 99 through 105 removed outlier: 3.583A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB1, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.937A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.649A 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 69 Processing sheet with id=AB4, first strand: chain 'I' and resid 66 through 69 removed outlier: 6.258A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU I 100 " --> pdb=" O GLN I 120 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN I 120 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.672A pdb=" N ILE I 177 " --> pdb=" O GLY I 154 " (cutoff:3.500A) 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 250 through 251 removed outlier: 4.379A pdb=" N ARG I 267 " --> pdb=" O ALA I 251 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.786A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.961A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 599 through 606 removed outlier: 5.235A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 718 removed outlier: 6.552A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP I 781 " --> pdb=" O ALA I 718 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 748 through 752 removed outlier: 5.763A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'I' and resid 1096 through 1098 removed outlier: 3.556A pdb=" N MET I 800 " --> pdb=" O MET I1230 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET I1230 " --> pdb=" O MET I 800 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 830 through 838 removed outlier: 6.441A pdb=" N LYS I1051 " --> pdb=" O VAL I 931 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL I 931 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR I1053 " --> pdb=" O ILE I 929 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR I 927 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.788A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 1065 through 1066 Processing sheet with id=AD3, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 3.692A pdb=" N SER J 353 " --> pdb=" O MET J 466 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1335 through 1338 Processing sheet with id=AD5, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.302A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 144 through 145 Processing sheet with id=AD7, first strand: chain 'J' and resid 356 through 357 removed outlier: 6.107A pdb=" N THR J 356 " --> pdb=" O LEU J 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'J' and resid 547 through 556 removed outlier: 3.653A pdb=" N GLU J 556 " --> pdb=" O VAL J 564 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 706 through 708 Processing sheet with id=AE1, first strand: chain 'J' and resid 842 through 843 removed outlier: 3.882A pdb=" N ARG J 842 " --> pdb=" O LEU J 864 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 949 through 951 removed outlier: 3.603A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 991 through 997 removed outlier: 4.795A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER J 961 " --> pdb=" O GLU J 981 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS J 959 " --> pdb=" O LYS J 983 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE J 985 " --> pdb=" O SER J 957 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU J1009 " --> pdb=" O ILE J 958 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 1034 through 1036 Processing sheet with id=AE5, first strand: chain 'J' and resid 1046 through 1047 removed outlier: 3.635A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1161 through 1162 Processing sheet with id=AE7, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.297A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 963 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 7.46 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4499 1.31 - 1.44: 6988 1.44 - 1.56: 15532 1.56 - 1.69: 183 1.69 - 1.81: 184 Bond restraints: 27386 Sorted by residual: bond pdb=" CA ARG J 425 " pdb=" C ARG J 425 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.25e-02 6.40e+03 2.16e+01 bond pdb=" C ARG J 425 " pdb=" O ARG J 425 " ideal model delta sigma weight residual 1.234 1.191 0.043 1.17e-02 7.31e+03 1.36e+01 bond pdb=" CA ARG J 425 " pdb=" CB ARG J 425 " ideal model delta sigma weight residual 1.530 1.475 0.055 1.58e-02 4.01e+03 1.22e+01 bond pdb=" C3' DA A 28 " pdb=" C2' DA A 28 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT B 12 " pdb=" C2' DT B 12 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.40e+00 ... (remaining 27381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 36512 1.79 - 3.57: 779 3.57 - 5.36: 114 5.36 - 7.14: 9 7.14 - 8.93: 2 Bond angle restraints: 37416 Sorted by residual: angle pdb=" N VAL I1254 " pdb=" CA VAL I1254 " pdb=" C VAL I1254 " ideal model delta sigma weight residual 112.29 108.01 4.28 9.40e-01 1.13e+00 2.07e+01 angle pdb=" N3 DT B 8 " pdb=" C4 DT B 8 " pdb=" O4 DT B 8 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT B 13 " pdb=" C4 DT B 13 " pdb=" O4 DT B 13 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT B 12 " pdb=" C4 DT B 12 " pdb=" O4 DT B 12 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT B 19 " pdb=" C4 DT B 19 " pdb=" O4 DT B 19 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 37411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.49: 15949 33.49 - 66.98: 605 66.98 - 100.47: 44 100.47 - 133.96: 0 133.96 - 167.45: 3 Dihedral angle restraints: 16601 sinusoidal: 7498 harmonic: 9103 Sorted by residual: dihedral pdb=" C4' U R 24 " pdb=" C3' U R 24 " pdb=" C2' U R 24 " pdb=" C1' U R 24 " ideal model delta sinusoidal sigma weight residual 36.34 -36.39 72.73 1 3.10e+00 1.04e-01 7.02e+02 dihedral pdb=" C4' G R 38 " pdb=" C3' G R 38 " pdb=" C2' G R 38 " pdb=" C1' G R 38 " ideal model delta sinusoidal sigma weight residual 36.34 -35.89 72.24 1 3.10e+00 1.04e-01 6.94e+02 dihedral pdb=" C4' A R 16 " pdb=" C3' A R 16 " pdb=" C2' A R 16 " pdb=" C1' A R 16 " ideal model delta sinusoidal sigma weight residual 36.34 -35.86 72.21 1 3.10e+00 1.04e-01 6.94e+02 ... (remaining 16598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3785 0.069 - 0.138: 446 0.138 - 0.208: 12 0.208 - 0.277: 62 0.277 - 0.346: 4 Chirality restraints: 4309 Sorted by residual: chirality pdb=" P A R 3 " pdb=" OP1 A R 3 " pdb=" OP2 A R 3 " pdb=" O5' A R 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.52 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" P G R 37 " pdb=" OP1 G R 37 " pdb=" OP2 G R 37 " pdb=" O5' G R 37 " both_signs ideal model delta sigma weight residual True 2.17 -2.46 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C2' G R 38 " pdb=" C3' G R 38 " pdb=" O2' G R 38 " pdb=" C1' G R 38 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 4306 not shown) Planarity restraints: 4556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN J 424 " -0.013 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C ASN J 424 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN J 424 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG J 425 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G R 46 " -0.031 2.00e-02 2.50e+03 1.32e-02 5.26e+00 pdb=" N9 G R 46 " 0.031 2.00e-02 2.50e+03 pdb=" C8 G R 46 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G R 46 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G R 46 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G R 46 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G R 46 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G R 46 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G R 46 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G R 46 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G R 46 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G R 46 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY J 358 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO J 359 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO J 359 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 359 " -0.025 5.00e-02 4.00e+02 ... (remaining 4553 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 308 2.58 - 3.16: 23528 3.16 - 3.74: 44403 3.74 - 4.32: 59592 4.32 - 4.90: 95788 Nonbonded interactions: 223619 Sorted by model distance: nonbonded pdb=" NZ LYS I1306 " pdb=" O2' C R 17 " model vdw 2.004 3.120 nonbonded pdb=" N1 DG A 26 " pdb=" OE2 GLU I 541 " model vdw 2.049 3.120 nonbonded pdb=" OP1 DT B 19 " pdb=" CG LYS I1262 " model vdw 2.055 3.440 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1401 " model vdw 2.087 2.170 nonbonded pdb=" OH TYR I 123 " pdb=" OE2 GLU I 126 " model vdw 2.182 3.040 ... (remaining 223614 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: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 28.730 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.003 0.058 27386 Z= 0.201 Angle : 0.632 8.927 37416 Z= 0.380 Chirality : 0.052 0.346 4309 Planarity : 0.004 0.046 4556 Dihedral : 16.143 167.451 10745 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.31 % Favored : 91.59 % Rotamer: Outliers : 1.07 % Allowed : 7.11 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.15), residues: 3152 helix: -0.07 (0.16), residues: 1087 sheet: -2.43 (0.27), residues: 365 loop : -1.82 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 101 TYR 0.013 0.001 TYR I1281 PHE 0.012 0.001 PHE J 260 TRP 0.012 0.001 TRP J 580 HIS 0.003 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.20 (27386) covalent geometry : angle 0.63224 / 0.38 (37416) hydrogen bonds : bond 0.18961 / 21.17 ( 1024) hydrogen bonds : angle 7.06155 / 7.09 ( 2838) *********************** 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 580 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 551 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 41 ASN cc_start: 0.8576 (t0) cc_final: 0.8335 (t0) REVERT: G 75 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8343 (tm-30) REVERT: G 194 GLN cc_start: 0.7245 (pp30) cc_final: 0.6959 (pp30) REVERT: H 100 LEU cc_start: 0.9175 (mp) cc_final: 0.8967 (mt) REVERT: H 185 TYR cc_start: 0.8681 (p90) cc_final: 0.8331 (p90) REVERT: I 84 GLU cc_start: 0.7882 (tp30) cc_final: 0.7393 (mm-30) REVERT: I 523 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6526 (mm-30) REVERT: I 568 ASN cc_start: 0.8396 (p0) cc_final: 0.8094 (p0) REVERT: I 654 ASP cc_start: 0.7373 (m-30) cc_final: 0.6939 (m-30) REVERT: I 739 ASP cc_start: 0.8279 (p0) cc_final: 0.7993 (p0) REVERT: I 820 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7732 (tm-30) REVERT: I 1018 TYR cc_start: 0.6946 (t80) cc_final: 0.6276 (m-80) REVERT: I 1023 HIS cc_start: 0.8008 (t-90) cc_final: 0.7770 (t-90) REVERT: I 1085 MET cc_start: 0.8727 (mmt) cc_final: 0.8494 (mmt) REVERT: I 1098 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8864 (mm) REVERT: I 1180 MET cc_start: 0.8904 (tpp) cc_final: 0.8387 (tpp) REVERT: I 1305 TYR cc_start: 0.8776 (t80) cc_final: 0.8548 (t80) REVERT: J 267 ASP cc_start: 0.8376 (p0) cc_final: 0.7891 (t70) REVERT: J 298 MET cc_start: 0.8439 (ptt) cc_final: 0.8189 (ptp) REVERT: J 698 MET cc_start: 0.9097 (mmm) cc_final: 0.8714 (tpp) REVERT: J 833 GLU cc_start: 0.6652 (mt-10) cc_final: 0.6451 (mt-10) REVERT: J 1121 LEU cc_start: 0.8639 (tp) cc_final: 0.8358 (mp) REVERT: K 8 ASP cc_start: 0.8414 (p0) cc_final: 0.7935 (p0) REVERT: K 47 THR cc_start: 0.9204 (m) cc_final: 0.8953 (m) outliers start: 29 outliers final: 6 residues processed: 574 average time/residue: 0.1872 time to fit residues: 165.6498 Evaluate side-chains 322 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 315 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 227 GLN H 84 ASN I 343 HIS I 462 ASN I 519 ASN ** I 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN I 659 GLN I1220 GLN ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN J 736 GLN J1010 GLN J1295 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.114643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.084859 restraints weight = 63238.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.087462 restraints weight = 34988.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.088033 restraints weight = 21683.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088652 restraints weight = 19111.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.088726 restraints weight = 16785.480| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27386 Z= 0.193 Angle : 0.888 20.597 37416 Z= 0.415 Chirality : 0.072 1.145 4309 Planarity : 0.005 0.053 4556 Dihedral : 15.081 166.309 4552 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.30 % Favored : 92.67 % Rotamer: Outliers : 2.55 % Allowed : 13.88 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.15), residues: 3152 helix: -0.17 (0.15), residues: 1106 sheet: -2.65 (0.26), residues: 346 loop : -1.77 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 101 TYR 0.032 0.002 TYR J 144 PHE 0.017 0.002 PHE I 253 TRP 0.015 0.002 TRP J1193 HIS 0.010 0.001 HIS I 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (27386) covalent geometry : angle 0.88782 / 0.42 (37416) hydrogen bonds : bond 0.05108 / 5.45 ( 1024) hydrogen bonds : angle 5.63125 / 5.88 ( 2838) *********************** 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 437 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 368 time to evaluate : 0.844 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 75 GLN cc_start: 0.9154 (tm-30) cc_final: 0.8333 (tm-30) REVERT: G 142 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7721 (mtm) REVERT: H 100 LEU cc_start: 0.9012 (mp) cc_final: 0.8811 (mt) REVERT: H 185 TYR cc_start: 0.8772 (p90) cc_final: 0.8336 (p90) REVERT: I 84 GLU cc_start: 0.8082 (tp30) cc_final: 0.7506 (mm-30) REVERT: I 163 LYS cc_start: 0.8415 (mmmt) cc_final: 0.8199 (tppt) REVERT: I 568 ASN cc_start: 0.8610 (p0) cc_final: 0.8122 (p0) REVERT: I 820 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7785 (tm-30) REVERT: I 1018 TYR cc_start: 0.7055 (t80) cc_final: 0.6342 (m-80) REVERT: I 1098 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8787 (mm) REVERT: I 1141 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9033 (tt) REVERT: I 1180 MET cc_start: 0.8988 (tpp) cc_final: 0.8422 (tpp) REVERT: I 1304 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8279 (ttm) REVERT: J 114 ILE cc_start: 0.8619 (mm) cc_final: 0.8227 (mp) REVERT: J 267 ASP cc_start: 0.8403 (p0) cc_final: 0.7901 (t70) REVERT: J 329 ASP cc_start: 0.8489 (m-30) cc_final: 0.8106 (m-30) REVERT: J 698 MET cc_start: 0.9024 (mmm) cc_final: 0.8791 (tpp) REVERT: J 833 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6459 (mt-10) REVERT: J 1121 LEU cc_start: 0.8645 (tp) cc_final: 0.8335 (mp) REVERT: K 63 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8964 (mm) outliers start: 69 outliers final: 30 residues processed: 410 average time/residue: 0.1609 time to fit residues: 108.0899 Evaluate side-chains 335 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 300 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 356 THR Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 63 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 252 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 chunk 287 optimal weight: 6.9990 chunk 82 optimal weight: 0.3980 chunk 297 optimal weight: 0.7980 chunk 269 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 227 GLN ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN I 513 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 604 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1314 GLN ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.114421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.084656 restraints weight = 63259.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.087495 restraints weight = 34822.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.088232 restraints weight = 20896.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.088294 restraints weight = 17687.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.088631 restraints weight = 17820.843| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27386 Z= 0.167 Angle : 0.737 12.968 37416 Z= 0.357 Chirality : 0.057 0.784 4309 Planarity : 0.004 0.053 4556 Dihedral : 15.201 160.853 4551 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.44 % Favored : 93.53 % Rotamer: Outliers : 3.41 % Allowed : 15.36 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.15), residues: 3152 helix: -0.10 (0.15), residues: 1111 sheet: -2.44 (0.26), residues: 368 loop : -1.74 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I1106 TYR 0.017 0.002 TYR J 140 PHE 0.024 0.001 PHE J 176 TRP 0.011 0.001 TRP J 580 HIS 0.007 0.001 HIS J1218 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (27386) covalent geometry : angle 0.73740 / 0.36 (37416) hydrogen bonds : bond 0.04667 / 5.03 ( 1024) hydrogen bonds : angle 5.34364 / 5.57 ( 2838) *********************** 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 429 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 337 time to evaluate : 0.967 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 75 GLN cc_start: 0.9161 (tm-30) cc_final: 0.8302 (tm-30) REVERT: G 142 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7656 (mtm) REVERT: G 185 TYR cc_start: 0.8661 (p90) cc_final: 0.8293 (p90) REVERT: G 217 ILE cc_start: 0.9516 (tp) cc_final: 0.9307 (tp) REVERT: H 100 LEU cc_start: 0.8862 (mp) cc_final: 0.8660 (mt) REVERT: H 185 TYR cc_start: 0.8787 (p90) cc_final: 0.8390 (p90) REVERT: I 84 GLU cc_start: 0.8069 (tp30) cc_final: 0.7489 (mm-30) REVERT: I 163 LYS cc_start: 0.8368 (mmmt) cc_final: 0.8126 (tptt) REVERT: I 395 TYR cc_start: 0.7765 (t80) cc_final: 0.7475 (t80) REVERT: I 693 LEU cc_start: 0.8646 (tp) cc_final: 0.8332 (mp) REVERT: I 820 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7837 (tm-30) REVERT: I 882 ILE cc_start: 0.8467 (mp) cc_final: 0.8040 (tt) REVERT: I 1018 TYR cc_start: 0.7109 (t80) cc_final: 0.6379 (m-80) REVERT: I 1098 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8690 (mm) REVERT: I 1180 MET cc_start: 0.8974 (tpp) cc_final: 0.8414 (tpp) REVERT: I 1274 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7544 (mm-30) REVERT: I 1304 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8222 (ttm) REVERT: J 115 TRP cc_start: 0.8378 (m-10) cc_final: 0.7928 (m100) REVERT: J 159 ILE cc_start: 0.8526 (tt) cc_final: 0.8195 (tt) REVERT: J 329 ASP cc_start: 0.8511 (m-30) cc_final: 0.8080 (m-30) REVERT: J 833 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6507 (mt-10) REVERT: J 1003 LEU cc_start: 0.8298 (tp) cc_final: 0.8012 (tt) REVERT: J 1121 LEU cc_start: 0.8690 (tp) cc_final: 0.8372 (mp) REVERT: J 1317 GLU cc_start: 0.7830 (pm20) cc_final: 0.7512 (pm20) REVERT: K 8 ASP cc_start: 0.8420 (p0) cc_final: 0.7598 (p0) REVERT: K 75 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7886 (tm-30) outliers start: 92 outliers final: 42 residues processed: 402 average time/residue: 0.1468 time to fit residues: 97.5680 Evaluate side-chains 345 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 300 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 662 SER Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1195 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 46 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 31 optimal weight: 5.9990 chunk 230 optimal weight: 0.9990 chunk 199 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 284 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 227 GLN ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 HIS ** I 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1061 GLN ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.112285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.082107 restraints weight = 63363.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.084334 restraints weight = 34006.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.085795 restraints weight = 22992.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.086555 restraints weight = 18129.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.087176 restraints weight = 15965.994| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 27386 Z= 0.226 Angle : 0.724 9.745 37416 Z= 0.359 Chirality : 0.051 0.495 4309 Planarity : 0.005 0.054 4556 Dihedral : 15.209 160.902 4551 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.07 % Allowed : 16.18 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.15), residues: 3152 helix: -0.00 (0.15), residues: 1113 sheet: -2.50 (0.26), residues: 358 loop : -1.68 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I1106 TYR 0.025 0.002 TYR J 140 PHE 0.023 0.002 PHE J 176 TRP 0.010 0.001 TRP J 580 HIS 0.009 0.001 HIS J1218 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 (27386) covalent geometry : angle 0.72405 / 0.36 (37416) hydrogen bonds : bond 0.04525 / 4.85 ( 1024) hydrogen bonds : angle 5.22428 / 5.55 ( 2838) *********************** 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 428 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 318 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 GLU cc_start: 0.7668 (tp30) cc_final: 0.7123 (tt0) REVERT: G 75 GLN cc_start: 0.9266 (tm-30) cc_final: 0.8304 (tm-30) REVERT: G 142 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7779 (mtm) REVERT: G 217 ILE cc_start: 0.9539 (OUTLIER) cc_final: 0.9310 (tp) REVERT: H 185 TYR cc_start: 0.8867 (p90) cc_final: 0.8511 (p90) REVERT: I 84 GLU cc_start: 0.8191 (tp30) cc_final: 0.7617 (mm-30) REVERT: I 142 GLU cc_start: 0.7528 (tt0) cc_final: 0.7225 (tt0) REVERT: I 163 LYS cc_start: 0.8341 (mmmt) cc_final: 0.8127 (tppt) REVERT: I 562 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8497 (tp30) REVERT: I 693 LEU cc_start: 0.8779 (tp) cc_final: 0.8433 (mp) REVERT: I 788 SER cc_start: 0.9040 (m) cc_final: 0.8474 (p) REVERT: I 820 GLU cc_start: 0.8496 (tm-30) cc_final: 0.7916 (tm-30) REVERT: I 882 ILE cc_start: 0.8526 (mp) cc_final: 0.8106 (tt) REVERT: I 1018 TYR cc_start: 0.7351 (t80) cc_final: 0.6439 (m-80) REVERT: I 1098 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8766 (mm) REVERT: I 1180 MET cc_start: 0.9024 (tpp) cc_final: 0.8482 (tpp) REVERT: I 1274 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7798 (mm-30) REVERT: I 1304 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8417 (ttm) REVERT: J 194 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9052 (mm) REVERT: J 267 ASP cc_start: 0.8550 (p0) cc_final: 0.7954 (t70) REVERT: J 329 ASP cc_start: 0.8567 (m-30) cc_final: 0.8107 (m-30) REVERT: J 460 ASP cc_start: 0.7971 (m-30) cc_final: 0.7729 (t0) REVERT: J 698 MET cc_start: 0.9074 (mmm) cc_final: 0.8793 (mmm) REVERT: J 833 GLU cc_start: 0.6769 (mt-10) cc_final: 0.6506 (mt-10) REVERT: J 1121 LEU cc_start: 0.8677 (tp) cc_final: 0.8328 (mp) REVERT: K 30 MET cc_start: 0.8530 (tmm) cc_final: 0.8330 (tmm) REVERT: K 75 GLN cc_start: 0.8094 (tm-30) cc_final: 0.7776 (tm-30) outliers start: 110 outliers final: 60 residues processed: 394 average time/residue: 0.1486 time to fit residues: 97.5068 Evaluate side-chains 357 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 292 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 662 SER Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 887 VAL Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1176 LEU Chi-restraints excluded: chain I residue 1195 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 194 LEU Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1141 VAL Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 46 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 96 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 232 optimal weight: 0.0980 chunk 125 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 89 optimal weight: 0.1980 chunk 148 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 173 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 227 GLN ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 513 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.114832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.084669 restraints weight = 63389.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.086962 restraints weight = 33866.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.088461 restraints weight = 22829.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.089289 restraints weight = 17997.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.089940 restraints weight = 15755.813| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27386 Z= 0.130 Angle : 0.673 12.979 37416 Z= 0.332 Chirality : 0.049 0.402 4309 Planarity : 0.004 0.056 4556 Dihedral : 15.137 162.893 4551 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.22 % Allowed : 17.88 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.15), residues: 3152 helix: 0.15 (0.16), residues: 1102 sheet: -2.27 (0.26), residues: 361 loop : -1.61 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 312 TYR 0.028 0.001 TYR G 185 PHE 0.027 0.001 PHE J 176 TRP 0.010 0.001 TRP I 807 HIS 0.004 0.001 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (27386) covalent geometry : angle 0.67332 / 0.33 (37416) hydrogen bonds : bond 0.04172 / 4.48 ( 1024) hydrogen bonds : angle 5.04573 / 5.28 ( 2838) *********************** 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 423 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 336 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 GLU cc_start: 0.7518 (tp30) cc_final: 0.6951 (tt0) REVERT: G 75 GLN cc_start: 0.9173 (tm-30) cc_final: 0.8295 (tm-30) REVERT: G 142 MET cc_start: 0.8180 (mtp) cc_final: 0.7626 (mtm) REVERT: G 217 ILE cc_start: 0.9507 (tp) cc_final: 0.9278 (tp) REVERT: H 41 ASN cc_start: 0.8186 (t0) cc_final: 0.7678 (t0) REVERT: H 185 TYR cc_start: 0.8763 (p90) cc_final: 0.8481 (p90) REVERT: I 84 GLU cc_start: 0.7985 (tp30) cc_final: 0.7434 (mm-30) REVERT: I 142 GLU cc_start: 0.7346 (tt0) cc_final: 0.7101 (tt0) REVERT: I 163 LYS cc_start: 0.8307 (mmmt) cc_final: 0.8087 (tppt) REVERT: I 315 MET cc_start: 0.7808 (mmm) cc_final: 0.7395 (mmm) REVERT: I 523 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7338 (mm-30) REVERT: I 611 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8270 (tt0) REVERT: I 693 LEU cc_start: 0.8657 (tp) cc_final: 0.8391 (mp) REVERT: I 788 SER cc_start: 0.8920 (m) cc_final: 0.8403 (p) REVERT: I 820 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7834 (tm-30) REVERT: I 882 ILE cc_start: 0.8565 (mp) cc_final: 0.8177 (tt) REVERT: I 1018 TYR cc_start: 0.7249 (t80) cc_final: 0.6494 (m-80) REVERT: I 1098 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8618 (mm) REVERT: I 1180 MET cc_start: 0.8945 (tpp) cc_final: 0.8236 (tpp) REVERT: J 115 TRP cc_start: 0.8216 (m-10) cc_final: 0.7821 (m100) REVERT: J 267 ASP cc_start: 0.8454 (p0) cc_final: 0.7713 (t70) REVERT: J 329 ASP cc_start: 0.8499 (m-30) cc_final: 0.8045 (m-30) REVERT: J 698 MET cc_start: 0.9095 (mmm) cc_final: 0.8810 (mmm) REVERT: J 930 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8552 (tp) REVERT: J 1121 LEU cc_start: 0.8753 (tp) cc_final: 0.8412 (mp) REVERT: J 1281 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7354 (tt0) REVERT: K 8 ASP cc_start: 0.8122 (p0) cc_final: 0.7802 (p0) outliers start: 87 outliers final: 51 residues processed: 399 average time/residue: 0.1504 time to fit residues: 100.1485 Evaluate side-chains 354 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 300 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 662 SER Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1012 GLU Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain K residue 4 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 149 optimal weight: 5.9990 chunk 284 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 292 optimal weight: 7.9990 chunk 244 optimal weight: 0.5980 chunk 302 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 275 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 299 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 513 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.112266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.082010 restraints weight = 63420.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.084207 restraints weight = 34344.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.085676 restraints weight = 23322.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.086558 restraints weight = 18425.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.087123 restraints weight = 16075.281| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 27386 Z= 0.211 Angle : 0.703 13.122 37416 Z= 0.347 Chirality : 0.049 0.360 4309 Planarity : 0.004 0.059 4556 Dihedral : 15.157 165.591 4551 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.70 % Allowed : 18.59 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.15), residues: 3152 helix: 0.12 (0.16), residues: 1124 sheet: -2.24 (0.26), residues: 374 loop : -1.58 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 67 TYR 0.031 0.002 TYR J 140 PHE 0.023 0.002 PHE J 461 TRP 0.014 0.001 TRP J 580 HIS 0.005 0.001 HIS I1237 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (27386) covalent geometry : angle 0.70321 / 0.35 (37416) hydrogen bonds : bond 0.04287 / 4.58 ( 1024) hydrogen bonds : angle 5.04601 / 5.34 ( 2838) *********************** 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 413 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 313 time to evaluate : 0.667 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 29 GLU cc_start: 0.7641 (tp30) cc_final: 0.7090 (tt0) REVERT: G 75 GLN cc_start: 0.9203 (tm-30) cc_final: 0.8282 (tm-30) REVERT: G 142 MET cc_start: 0.8209 (mtp) cc_final: 0.7673 (mtm) REVERT: G 217 ILE cc_start: 0.9543 (tp) cc_final: 0.9302 (tp) REVERT: H 185 TYR cc_start: 0.8831 (p90) cc_final: 0.8538 (p90) REVERT: I 84 GLU cc_start: 0.8038 (tp30) cc_final: 0.7502 (mm-30) REVERT: I 142 GLU cc_start: 0.7429 (tt0) cc_final: 0.7221 (tt0) REVERT: I 262 TYR cc_start: 0.6568 (m-10) cc_final: 0.6330 (m-10) REVERT: I 562 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8452 (tp30) REVERT: I 611 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8284 (tt0) REVERT: I 693 LEU cc_start: 0.8765 (tp) cc_final: 0.8445 (mp) REVERT: I 788 SER cc_start: 0.9041 (m) cc_final: 0.8500 (p) REVERT: I 820 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7867 (tm-30) REVERT: I 882 ILE cc_start: 0.8562 (mp) cc_final: 0.8145 (tt) REVERT: I 1018 TYR cc_start: 0.7413 (t80) cc_final: 0.6441 (m-80) REVERT: I 1098 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8787 (mm) REVERT: I 1180 MET cc_start: 0.9004 (tpp) cc_final: 0.8341 (tpp) REVERT: J 267 ASP cc_start: 0.8479 (p0) cc_final: 0.7793 (t70) REVERT: J 329 ASP cc_start: 0.8499 (m-30) cc_final: 0.8066 (m-30) REVERT: J 698 MET cc_start: 0.9135 (mmm) cc_final: 0.8733 (mmm) REVERT: J 930 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8585 (tp) REVERT: J 1121 LEU cc_start: 0.8634 (tp) cc_final: 0.8432 (tp) REVERT: J 1281 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7315 (tt0) REVERT: K 8 ASP cc_start: 0.8117 (p0) cc_final: 0.7851 (p0) REVERT: K 30 MET cc_start: 0.8419 (tmm) cc_final: 0.8219 (tmm) outliers start: 100 outliers final: 66 residues processed: 385 average time/residue: 0.1425 time to fit residues: 92.7777 Evaluate side-chains 363 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 294 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 222 THR Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 46 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 319 optimal weight: 30.0000 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 237 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 1 optimal weight: 30.0000 chunk 168 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 41 ASN H 132 HIS ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 526 HIS ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.114129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.083981 restraints weight = 63287.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.086243 restraints weight = 33963.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.087716 restraints weight = 22967.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.088657 restraints weight = 18131.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.089123 restraints weight = 15790.911| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27386 Z= 0.141 Angle : 0.670 9.782 37416 Z= 0.330 Chirality : 0.048 0.304 4309 Planarity : 0.004 0.060 4556 Dihedral : 15.085 166.048 4548 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.07 % Allowed : 19.29 % Favored : 77.64 % 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 are not related in a simple way. whole: -1.46 (0.15), residues: 3152 helix: 0.25 (0.16), residues: 1120 sheet: -2.15 (0.26), residues: 368 loop : -1.54 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 67 TYR 0.026 0.001 TYR J 140 PHE 0.019 0.001 PHE G 35 TRP 0.010 0.001 TRP J 580 HIS 0.004 0.001 HIS J 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (27386) covalent geometry : angle 0.66994 / 0.33 (37416) hydrogen bonds : bond 0.04094 / 4.42 ( 1024) hydrogen bonds : angle 4.92136 / 5.14 ( 2838) *********************** 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 409 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 326 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 GLU cc_start: 0.7606 (tp30) cc_final: 0.7044 (tt0) REVERT: G 75 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8312 (tm-30) REVERT: G 142 MET cc_start: 0.8170 (mtp) cc_final: 0.7634 (mtm) REVERT: G 217 ILE cc_start: 0.9522 (tp) cc_final: 0.9284 (tp) REVERT: H 41 ASN cc_start: 0.8233 (t0) cc_final: 0.7791 (t0) REVERT: H 185 TYR cc_start: 0.8759 (p90) cc_final: 0.8500 (p90) REVERT: I 84 GLU cc_start: 0.8000 (tp30) cc_final: 0.7472 (mm-30) REVERT: I 262 TYR cc_start: 0.6481 (m-10) cc_final: 0.6228 (m-10) REVERT: I 315 MET cc_start: 0.7773 (mmm) cc_final: 0.7333 (mmm) REVERT: I 611 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8286 (tt0) REVERT: I 693 LEU cc_start: 0.8679 (tp) cc_final: 0.8435 (mp) REVERT: I 788 SER cc_start: 0.8954 (m) cc_final: 0.8401 (p) REVERT: I 820 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7835 (tm-30) REVERT: I 882 ILE cc_start: 0.8541 (mp) cc_final: 0.8167 (tt) REVERT: I 1018 TYR cc_start: 0.7448 (t80) cc_final: 0.6419 (m-80) REVERT: I 1098 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8676 (mm) REVERT: I 1180 MET cc_start: 0.8973 (tpp) cc_final: 0.8271 (tpp) REVERT: I 1274 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7488 (mm-30) REVERT: I 1290 MET cc_start: 0.8654 (mmt) cc_final: 0.8414 (mmt) REVERT: J 115 TRP cc_start: 0.8146 (m-10) cc_final: 0.7920 (m100) REVERT: J 267 ASP cc_start: 0.8439 (p0) cc_final: 0.7739 (t70) REVERT: J 329 ASP cc_start: 0.8466 (m-30) cc_final: 0.8018 (m-30) REVERT: J 534 GLU cc_start: 0.8528 (tt0) cc_final: 0.8271 (tt0) REVERT: J 581 MET cc_start: 0.8274 (mtm) cc_final: 0.7772 (mtm) REVERT: J 930 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8455 (tp) REVERT: J 1281 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7206 (tt0) REVERT: K 28 ARG cc_start: 0.7747 (mmt90) cc_final: 0.7426 (mmt180) outliers start: 83 outliers final: 58 residues processed: 385 average time/residue: 0.1406 time to fit residues: 91.0659 Evaluate side-chains 362 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 301 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 356 THR Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1343 GLU Chi-restraints excluded: chain K residue 4 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 49 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 291 optimal weight: 30.0000 chunk 122 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 222 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.113624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.084041 restraints weight = 63791.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.086318 restraints weight = 34926.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.087149 restraints weight = 21631.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.087330 restraints weight = 19582.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.087371 restraints weight = 17898.970| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27386 Z= 0.158 Angle : 0.672 8.939 37416 Z= 0.331 Chirality : 0.047 0.296 4309 Planarity : 0.004 0.071 4556 Dihedral : 15.061 167.151 4548 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.07 % Allowed : 19.92 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.15), residues: 3152 helix: 0.26 (0.16), residues: 1132 sheet: -2.06 (0.27), residues: 358 loop : -1.49 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 731 TYR 0.024 0.001 TYR J 140 PHE 0.023 0.001 PHE J1325 TRP 0.011 0.001 TRP J 580 HIS 0.005 0.001 HIS I 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (27386) covalent geometry : angle 0.67235 / 0.33 (37416) hydrogen bonds : bond 0.04064 / 4.39 ( 1024) hydrogen bonds : angle 4.88497 / 5.12 ( 2838) *********************** 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 401 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 318 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 GLU cc_start: 0.7652 (tp30) cc_final: 0.7095 (tt0) REVERT: G 31 LEU cc_start: 0.8698 (tp) cc_final: 0.8472 (tt) REVERT: G 75 GLN cc_start: 0.9175 (tm-30) cc_final: 0.8294 (tm-30) REVERT: G 142 MET cc_start: 0.8279 (mtp) cc_final: 0.7719 (mtm) REVERT: G 194 GLN cc_start: 0.7415 (pm20) cc_final: 0.7172 (pm20) REVERT: G 217 ILE cc_start: 0.9531 (tp) cc_final: 0.9276 (tp) REVERT: H 41 ASN cc_start: 0.8282 (t0) cc_final: 0.7804 (t0) REVERT: H 51 MET cc_start: 0.8741 (mpp) cc_final: 0.8525 (mpp) REVERT: H 185 TYR cc_start: 0.8811 (p90) cc_final: 0.8551 (p90) REVERT: I 84 GLU cc_start: 0.8176 (tp30) cc_final: 0.7598 (mm-30) REVERT: I 262 TYR cc_start: 0.6476 (m-10) cc_final: 0.6163 (m-10) REVERT: I 693 LEU cc_start: 0.8710 (tp) cc_final: 0.8433 (mp) REVERT: I 788 SER cc_start: 0.8976 (m) cc_final: 0.8421 (p) REVERT: I 820 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7899 (tm-30) REVERT: I 882 ILE cc_start: 0.8572 (mp) cc_final: 0.8168 (tt) REVERT: I 1018 TYR cc_start: 0.7501 (t80) cc_final: 0.6369 (m-80) REVERT: I 1098 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8630 (mm) REVERT: I 1180 MET cc_start: 0.9008 (tpp) cc_final: 0.8308 (tpp) REVERT: I 1274 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7486 (mm-30) REVERT: J 115 TRP cc_start: 0.8279 (m-10) cc_final: 0.7945 (m100) REVERT: J 241 VAL cc_start: 0.9514 (t) cc_final: 0.9309 (m) REVERT: J 267 ASP cc_start: 0.8572 (p0) cc_final: 0.7850 (t70) REVERT: J 329 ASP cc_start: 0.8576 (m-30) cc_final: 0.8071 (m-30) REVERT: J 534 GLU cc_start: 0.8578 (tt0) cc_final: 0.8318 (tt0) REVERT: J 581 MET cc_start: 0.8286 (mtm) cc_final: 0.7805 (mtm) REVERT: J 930 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8580 (tp) REVERT: J 1121 LEU cc_start: 0.8641 (tp) cc_final: 0.8313 (mp) REVERT: J 1281 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7310 (tt0) outliers start: 83 outliers final: 66 residues processed: 377 average time/residue: 0.1427 time to fit residues: 90.8077 Evaluate side-chains 371 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 302 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 662 SER Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 454 CYS Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain K residue 4 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 218 optimal weight: 4.9990 chunk 276 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 152 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 210 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 227 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 568 ASN I1061 GLN ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS K 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.113551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.085626 restraints weight = 63504.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.086549 restraints weight = 37441.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.088085 restraints weight = 27883.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.088160 restraints weight = 24707.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.087987 restraints weight = 20670.480| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27386 Z= 0.164 Angle : 0.682 9.833 37416 Z= 0.336 Chirality : 0.047 0.294 4309 Planarity : 0.004 0.051 4556 Dihedral : 15.040 167.830 4548 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.89 % Allowed : 20.47 % Favored : 76.64 % 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 are not related in a simple way. whole: -1.36 (0.15), residues: 3152 helix: 0.25 (0.16), residues: 1130 sheet: -1.99 (0.26), residues: 377 loop : -1.45 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 709 TYR 0.022 0.001 TYR J 140 PHE 0.020 0.001 PHE J1325 TRP 0.014 0.001 TRP J 115 HIS 0.004 0.001 HIS J 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (27386) covalent geometry : angle 0.68160 / 0.34 (37416) hydrogen bonds : bond 0.04056 / 4.39 ( 1024) hydrogen bonds : angle 4.86766 / 5.12 ( 2838) *********************** 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 379 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 301 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 GLU cc_start: 0.7487 (tp30) cc_final: 0.6954 (tt0) REVERT: G 31 LEU cc_start: 0.8633 (tp) cc_final: 0.8401 (tt) REVERT: G 75 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8300 (tm-30) REVERT: G 142 MET cc_start: 0.8044 (mtp) cc_final: 0.7443 (mtm) REVERT: G 194 GLN cc_start: 0.7363 (pm20) cc_final: 0.7058 (pm20) REVERT: G 217 ILE cc_start: 0.9513 (tp) cc_final: 0.9268 (tp) REVERT: H 185 TYR cc_start: 0.8760 (p90) cc_final: 0.8531 (p90) REVERT: I 84 GLU cc_start: 0.7801 (tp30) cc_final: 0.7366 (mm-30) REVERT: I 262 TYR cc_start: 0.6503 (m-10) cc_final: 0.5885 (m-10) REVERT: I 315 MET cc_start: 0.7712 (mmm) cc_final: 0.7211 (mmm) REVERT: I 568 ASN cc_start: 0.9204 (OUTLIER) cc_final: 0.8900 (p0) REVERT: I 693 LEU cc_start: 0.8663 (tp) cc_final: 0.8425 (mp) REVERT: I 788 SER cc_start: 0.8943 (m) cc_final: 0.8394 (p) REVERT: I 820 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7847 (tm-30) REVERT: I 882 ILE cc_start: 0.8523 (mp) cc_final: 0.8179 (tt) REVERT: I 1018 TYR cc_start: 0.7468 (t80) cc_final: 0.6366 (m-80) REVERT: I 1098 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8640 (mm) REVERT: I 1180 MET cc_start: 0.8951 (tpp) cc_final: 0.8249 (tpp) REVERT: I 1290 MET cc_start: 0.8555 (mmt) cc_final: 0.8271 (mmt) REVERT: J 115 TRP cc_start: 0.8127 (m-10) cc_final: 0.7850 (m-10) REVERT: J 241 VAL cc_start: 0.9418 (t) cc_final: 0.9210 (m) REVERT: J 267 ASP cc_start: 0.8399 (p0) cc_final: 0.7714 (t70) REVERT: J 329 ASP cc_start: 0.8337 (m-30) cc_final: 0.7958 (m-30) REVERT: J 460 ASP cc_start: 0.7736 (m-30) cc_final: 0.7484 (m-30) REVERT: J 534 GLU cc_start: 0.8399 (tt0) cc_final: 0.8104 (tt0) REVERT: J 581 MET cc_start: 0.8180 (mtm) cc_final: 0.7706 (mtm) REVERT: J 623 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7735 (mm-40) REVERT: J 930 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8553 (tp) REVERT: J 1121 LEU cc_start: 0.8561 (tp) cc_final: 0.8304 (mp) REVERT: J 1189 MET cc_start: 0.8406 (mmm) cc_final: 0.7951 (mmm) REVERT: J 1281 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7056 (tt0) outliers start: 78 outliers final: 63 residues processed: 358 average time/residue: 0.1346 time to fit residues: 82.4545 Evaluate side-chains 357 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 290 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 568 ASN Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1295 SER Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain K residue 4 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 188 optimal weight: 0.7980 chunk 303 optimal weight: 9.9990 chunk 287 optimal weight: 9.9990 chunk 42 optimal weight: 0.0980 chunk 147 optimal weight: 3.9990 chunk 268 optimal weight: 0.5980 chunk 311 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 213 optimal weight: 0.4980 chunk 133 optimal weight: 9.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.114970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.085923 restraints weight = 63260.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.087643 restraints weight = 35052.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.088396 restraints weight = 23087.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.088707 restraints weight = 21208.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.088667 restraints weight = 18843.576| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27386 Z= 0.129 Angle : 0.679 11.262 37416 Z= 0.333 Chirality : 0.047 0.285 4309 Planarity : 0.004 0.050 4556 Dihedral : 14.991 168.042 4548 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.37 % Allowed : 21.07 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.15), residues: 3152 helix: 0.29 (0.16), residues: 1125 sheet: -2.01 (0.26), residues: 370 loop : -1.42 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 69 TYR 0.024 0.001 TYR G 185 PHE 0.029 0.001 PHE G 35 TRP 0.013 0.001 TRP J 580 HIS 0.004 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (27386) covalent geometry : angle 0.67941 / 0.33 (37416) hydrogen bonds : bond 0.03968 / 4.31 ( 1024) hydrogen bonds : angle 4.80095 / 5.03 ( 2838) ********************** 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 375 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 311 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 GLU cc_start: 0.7555 (tp30) cc_final: 0.6979 (tt0) REVERT: G 31 LEU cc_start: 0.8665 (tp) cc_final: 0.8431 (tt) REVERT: G 75 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8276 (tm-30) REVERT: G 142 MET cc_start: 0.8280 (mtp) cc_final: 0.7693 (mtm) REVERT: G 194 GLN cc_start: 0.7376 (pm20) cc_final: 0.7110 (pm20) REVERT: G 217 ILE cc_start: 0.9522 (tp) cc_final: 0.9281 (tp) REVERT: H 41 ASN cc_start: 0.8229 (t0) cc_final: 0.7762 (t0) REVERT: I 84 GLU cc_start: 0.8143 (tp30) cc_final: 0.7544 (mm-30) REVERT: I 262 TYR cc_start: 0.6460 (m-10) cc_final: 0.5889 (m-10) REVERT: I 315 MET cc_start: 0.7860 (mmm) cc_final: 0.7299 (mmm) REVERT: I 370 MET cc_start: 0.8537 (mmm) cc_final: 0.8254 (mmm) REVERT: I 693 LEU cc_start: 0.8657 (tp) cc_final: 0.8429 (mp) REVERT: I 788 SER cc_start: 0.8936 (m) cc_final: 0.8419 (p) REVERT: I 820 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8037 (tm-30) REVERT: I 882 ILE cc_start: 0.8605 (mp) cc_final: 0.8198 (tt) REVERT: I 1018 TYR cc_start: 0.7528 (t80) cc_final: 0.6375 (m-80) REVERT: I 1098 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8659 (mm) REVERT: I 1180 MET cc_start: 0.8977 (tpp) cc_final: 0.8332 (tpp) REVERT: I 1274 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7664 (mm-30) REVERT: I 1290 MET cc_start: 0.8704 (mmt) cc_final: 0.8389 (mmt) REVERT: J 115 TRP cc_start: 0.8206 (m-10) cc_final: 0.7663 (m100) REVERT: J 241 VAL cc_start: 0.9479 (t) cc_final: 0.9267 (m) REVERT: J 267 ASP cc_start: 0.8521 (p0) cc_final: 0.7747 (t70) REVERT: J 329 ASP cc_start: 0.8514 (m-30) cc_final: 0.8009 (m-30) REVERT: J 534 GLU cc_start: 0.8533 (tt0) cc_final: 0.8243 (tt0) REVERT: J 581 MET cc_start: 0.8146 (mtm) cc_final: 0.7674 (mtm) REVERT: J 930 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8586 (tp) REVERT: J 1121 LEU cc_start: 0.8662 (tp) cc_final: 0.8366 (mp) REVERT: J 1189 MET cc_start: 0.8601 (mmm) cc_final: 0.8178 (mmm) REVERT: J 1281 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7263 (tt0) REVERT: K 28 ARG cc_start: 0.7616 (mmt90) cc_final: 0.7310 (mmt180) outliers start: 64 outliers final: 58 residues processed: 356 average time/residue: 0.1378 time to fit residues: 82.5811 Evaluate side-chains 353 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 292 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 231 PHE Chi-restraints excluded: chain I residue 57 PHE Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 662 SER Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 702 THR Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 826 ASP Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 928 VAL Chi-restraints excluded: chain I residue 1021 LEU Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1077 SER Chi-restraints excluded: chain I residue 1097 VAL Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 166 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 747 MET Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1159 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1267 VAL Chi-restraints excluded: chain J residue 1281 GLU Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain K residue 4 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 275 optimal weight: 9.9990 chunk 192 optimal weight: 0.0020 chunk 320 optimal weight: 40.0000 chunk 39 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 315 optimal weight: 0.9980 chunk 1 optimal weight: 30.0000 chunk 63 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 568 ASN ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 488 ASN K 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.114048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.084892 restraints weight = 63313.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.087030 restraints weight = 34823.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.087726 restraints weight = 22128.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.087937 restraints weight = 20791.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.087892 restraints weight = 18269.855| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27386 Z= 0.157 Angle : 0.686 10.183 37416 Z= 0.338 Chirality : 0.047 0.284 4309 Planarity : 0.004 0.050 4556 Dihedral : 14.971 168.583 4548 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.63 % Allowed : 21.36 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.15), residues: 3152 helix: 0.32 (0.16), residues: 1126 sheet: -1.92 (0.26), residues: 377 loop : -1.39 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I1033 TYR 0.042 0.001 TYR H 185 PHE 0.018 0.001 PHE J 176 TRP 0.012 0.001 TRP J 580 HIS 0.004 0.001 HIS J 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (27386) covalent geometry : angle 0.68630 / 0.34 (37416) hydrogen bonds : bond 0.03966 / 4.32 ( 1024) hydrogen bonds : angle 4.79770 / 5.05 ( 2838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4111.29 seconds wall clock time: 72 minutes 9.19 seconds (4329.19 seconds total)