Starting phenix.real_space_refine on Mon Jul 6 02:36:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9msj_48590/07_2026/9msj_48590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9msj_48590/07_2026/9msj_48590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9msj_48590/07_2026/9msj_48590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9msj_48590/07_2026/9msj_48590.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9msj_48590/07_2026/9msj_48590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9msj_48590/07_2026/9msj_48590.map" } resolution = 3.1 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= 0.001 sd= 0.023 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 109 5.49 5 Mg 1 5.21 5 S 116 5.16 5 C 19139 2.51 5 N 5467 2.21 5 O 6268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31102 Number of models: 1 Model: "" Number of chains: 16 Chain: "G" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2348 Classifications: {'peptide': 303} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 288} Chain breaks: 2 Chain: "H" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 213} Chain breaks: 1 Chain: "I" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10560 Classifications: {'peptide': 1339} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1282} Chain: "J" Number of atoms: 10657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1372, 10657 Classifications: {'peptide': 1372} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1316} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "M" Number of atoms: 2945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2945 Classifications: {'peptide': 371} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 353} Chain breaks: 1 Chain: "U" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1080 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain: "V" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1052 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain: "J" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "V" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "J" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15187 SG CYS J 70 52.056 62.413 130.996 1.00111.28 S ATOM 15201 SG CYS J 72 53.988 63.546 133.974 1.00127.07 S ATOM 15309 SG CYS J 85 50.535 64.320 133.953 1.00133.92 S ATOM 15333 SG CYS J 88 52.908 66.230 131.695 1.00114.39 S ATOM 21021 SG CYS J 814 31.376 88.898 70.044 1.00 83.42 S ATOM 21586 SG CYS J 888 34.394 88.597 72.014 1.00 77.06 S ATOM 21637 SG CYS J 895 32.892 85.902 70.090 1.00 71.86 S ATOM 21658 SG CYS J 898 34.348 88.514 68.250 1.00 88.43 S Time building chain proxies: 5.61, per 1000 atoms: 0.18 Number of scatterers: 31102 At special positions: 0 Unit cell: (160.82, 162.54, 171.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 116 16.00 P 109 15.00 Mg 1 11.99 O 6268 8.00 N 5467 7.00 C 19139 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: 2.15 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 12 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6832 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 51 sheets defined 41.3% alpha, 16.2% beta 40 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'G' and resid 35 through 50 removed outlier: 3.878A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 212 through 228 Processing helix chain 'G' and resid 228 through 234 removed outlier: 3.993A pdb=" N VAL G 232 " --> pdb=" O LEU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 255 removed outlier: 3.579A pdb=" N ARG G 255 " --> pdb=" O ILE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 260 Processing helix chain 'G' and resid 263 through 272 Processing helix chain 'G' and resid 277 through 284 removed outlier: 3.571A pdb=" N ARG G 284 " --> pdb=" O ASP G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 291 Processing helix chain 'G' and resid 296 through 310 removed outlier: 3.886A pdb=" N ARG G 310 " --> pdb=" O VAL G 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.587A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.570A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (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 226 Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.640A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.594A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL I 56 " --> pdb=" O ALA I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.992A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 293 removed outlier: 3.591A pdb=" N ALA I 293 " --> pdb=" O GLU I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 327 Processing helix chain 'I' and resid 345 through 354 removed outlier: 3.821A pdb=" N GLU I 349 " --> pdb=" O PRO I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 371 removed outlier: 3.539A pdb=" N LEU I 363 " --> pdb=" O ARG I 359 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.789A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 408 Processing helix chain 'I' and resid 421 through 437 removed outlier: 3.604A pdb=" N ILE I 425 " --> pdb=" O SER I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 479 removed outlier: 3.674A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU I 477 " --> pdb=" O ARG I 473 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG I 478 " --> pdb=" O ALA I 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.702A pdb=" N MET I 492 " --> pdb=" O MET I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.764A pdb=" N SER I 509 " --> pdb=" O PHE I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 545 through 549 removed outlier: 3.649A pdb=" N ASP I 549 " --> pdb=" O GLU I 546 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.665A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.815A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 662 through 667 Processing helix chain 'I' and resid 670 through 674 removed outlier: 3.547A pdb=" N HIS I 673 " --> pdb=" O PHE I 670 " (cutoff:3.500A) Processing helix chain 'I' and resid 675 through 687 removed outlier: 3.946A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 711 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 863 Processing helix chain 'I' and resid 896 through 907 Processing helix chain 'I' and resid 908 through 911 Processing helix chain 'I' and resid 942 through 982 removed outlier: 4.044A pdb=" N GLN I 955 " --> pdb=" O MET I 951 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA I 956 " --> pdb=" O GLN I 952 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG I 974 " --> pdb=" O GLY I 970 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 992 Processing helix chain 'I' and resid 993 through 999 removed outlier: 4.054A pdb=" N LEU I 998 " --> pdb=" O ARG I 994 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1037 removed outlier: 4.083A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1107 removed outlier: 3.886A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.640A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.526A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.811A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 removed outlier: 3.634A pdb=" N LYS I1242 " --> pdb=" O LEU I1238 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1282 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.895A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.793A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 11 Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.726A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 removed outlier: 3.543A pdb=" N SER J 119 " --> pdb=" O TRP J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 192 removed outlier: 3.675A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 208 Processing helix chain 'J' and resid 211 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 286 Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.601A pdb=" N VAL J 292 " --> pdb=" O PRO J 288 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN J 294 " --> pdb=" O ILE J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.682A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 388 removed outlier: 3.501A pdb=" N ARG J 388 " --> pdb=" O LYS J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 407 through 416 Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 removed outlier: 3.866A pdb=" N ASN J 489 " --> pdb=" O SER J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 4.002A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.757A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 removed outlier: 3.602A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.612A pdb=" N ASP J 622 " --> pdb=" O VAL J 618 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 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 removed outlier: 4.313A pdb=" N GLN J 739 " --> pdb=" O ALA J 735 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU J 740 " --> pdb=" O GLN J 736 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA J 741 " --> pdb=" O ILE J 737 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 789 removed outlier: 4.300A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR J 786 " --> pdb=" O GLY J 782 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA J 787 " --> pdb=" O LEU J 783 " (cutoff:3.500A) Processing helix chain 'J' and resid 790 through 805 removed outlier: 3.874A pdb=" N LEU J 796 " --> pdb=" O ASN J 792 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.800A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 removed outlier: 3.537A pdb=" N ASN J 875 " --> pdb=" O LEU J 871 " (cutoff:3.500A) Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 933 removed outlier: 3.623A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Proline residue: J 926 - end of helix Processing helix chain 'J' and resid 1068 through 1072 Processing helix chain 'J' and resid 1133 through 1136 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 1242 removed outlier: 3.616A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR J1241 " --> pdb=" O VAL J1237 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 removed outlier: 3.615A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.685A pdb=" N ALA J1294 " --> pdb=" O ARG J1290 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN J1295 " --> pdb=" O GLU J1291 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1314 Processing helix chain 'J' and resid 1319 through 1324 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1353 removed outlier: 3.601A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1359 through 1361 No H-bonds generated for 'chain 'J' and resid 1359 through 1361' Processing helix chain 'J' and resid 1362 through 1373 removed outlier: 3.837A pdb=" N HIS J1366 " --> pdb=" O GLY J1362 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 33 removed outlier: 3.708A pdb=" N VAL K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 removed outlier: 3.664A pdb=" N ALA K 50 " --> pdb=" O THR K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 80 Processing helix chain 'M' and resid 119 through 130 Processing helix chain 'M' and resid 134 through 147 removed outlier: 3.656A pdb=" N ALA M 147 " --> pdb=" O SER M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 166 removed outlier: 3.581A pdb=" N ILE M 161 " --> pdb=" O PRO M 157 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY M 166 " --> pdb=" O LEU M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 183 removed outlier: 3.966A pdb=" N VAL M 175 " --> pdb=" O ASP M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 204 Processing helix chain 'M' and resid 213 through 222 Processing helix chain 'M' and resid 224 through 229 Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 254 removed outlier: 3.530A pdb=" N LEU M 246 " --> pdb=" O LYS M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 263 removed outlier: 3.783A pdb=" N SER M 263 " --> pdb=" O PRO M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 291 through 294 Processing helix chain 'M' and resid 322 through 351 Processing helix chain 'M' and resid 351 through 358 removed outlier: 3.525A pdb=" N PHE M 355 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 375 removed outlier: 3.737A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 Processing helix chain 'M' and resid 417 through 429 Processing helix chain 'M' and resid 438 through 447 Processing helix chain 'M' and resid 454 through 466 Processing helix chain 'M' and resid 469 through 473 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 18 removed outlier: 6.716A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLN G 18 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 97 through 105 removed outlier: 7.748A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.665A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'H' and resid 15 through 20 removed outlier: 6.415A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 97 through 105 removed outlier: 8.092A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'H' and resid 108 through 111 removed outlier: 6.520A pdb=" N GLY H 108 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N HIS H 132 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.646A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.620A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.358A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 160 removed outlier: 3.658A pdb=" N LEU I 171 " --> pdb=" O ASP I 160 " (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 238 through 240 Processing sheet with id=AB9, first strand: chain 'I' and resid 255 through 257 removed outlier: 3.517A pdb=" N VAL I 263 " --> pdb=" O ILE I 255 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 301 through 302 removed outlier: 7.029A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.147A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N THR I 595 " --> pdb=" O THR I 600 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR I 600 " --> pdb=" O THR I 595 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC4, first strand: chain 'I' and resid 616 through 617 Processing sheet with id=AC5, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.837A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (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 768 through 769 Processing sheet with id=AC8, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.356A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 846 through 847 removed outlier: 6.122A pdb=" N ASP I 842 " --> pdb=" O VAL I1046 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL I1046 " --> pdb=" O ASP I 842 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 849 through 850 Processing sheet with id=AD3, first strand: chain 'I' and resid 882 through 884 Processing sheet with id=AD4, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD5, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AD6, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 4.065A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 103 through 112 removed outlier: 6.993A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.162A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 159 through 160 removed outlier: 7.177A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 253 through 254 Processing sheet with id=AE1, first strand: chain 'J' and resid 317 through 319 removed outlier: 4.548A pdb=" N SER J 319 " --> pdb=" O ARG J 322 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE3, first strand: chain 'J' and resid 704 through 707 Processing sheet with id=AE4, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE5, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE6, first strand: chain 'J' and resid 825 through 826 Processing sheet with id=AE7, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.578A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.172A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 991 through 997 removed outlier: 6.542A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS J 996 " --> pdb=" O THR J 980 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR J 980 " --> pdb=" O LYS J 996 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY J 956 " --> pdb=" O VAL J1011 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 6.527A pdb=" N MET J1025 " --> pdb=" O ARG J1123 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ARG J1123 " --> pdb=" O MET J1025 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL J1027 " --> pdb=" O LEU J1121 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AF3, first strand: chain 'J' and resid 1187 through 1188 Processing sheet with id=AF4, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.934A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 284 through 289 removed outlier: 6.758A pdb=" N VAL M 276 " --> pdb=" O HIS M 391 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 406 through 408 1237 hydrogen bonds defined for protein. 3450 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 94 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 7.27 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8896 1.33 - 1.45: 4874 1.45 - 1.57: 17555 1.57 - 1.69: 214 1.69 - 1.81: 201 Bond restraints: 31740 Sorted by residual: bond pdb=" C1' DT V 35 " pdb=" N1 DT V 35 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.06e+01 bond pdb=" C3' DA U 62 " pdb=" C2' DA U 62 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT V 47 " pdb=" C2' DT V 47 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DT V 48 " pdb=" C2' DT V 48 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.94e+00 bond pdb=" C3' DT V 53 " pdb=" C2' DT V 53 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.82e+00 ... (remaining 31735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 42135 1.42 - 2.84: 1105 2.84 - 4.26: 93 4.26 - 5.69: 18 5.69 - 7.11: 4 Bond angle restraints: 43355 Sorted by residual: angle pdb=" N3 DT V 42 " pdb=" C4 DT V 42 " pdb=" O4 DT V 42 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" O4' DT V 39 " pdb=" C4' DT V 39 " pdb=" C3' DT V 39 " ideal model delta sigma weight residual 106.00 103.39 2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT V 59 " pdb=" C4 DT V 59 " pdb=" O4 DT V 59 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT U 76 " pdb=" C4 DT U 76 " pdb=" O4 DT U 76 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT V 22 " pdb=" C4 DT V 22 " pdb=" O4 DT V 22 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 43350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 18672 35.26 - 70.51: 594 70.51 - 105.77: 16 105.77 - 141.03: 2 141.03 - 176.29: 4 Dihedral angle restraints: 19288 sinusoidal: 8682 harmonic: 10606 Sorted by residual: dihedral pdb=" CA ARG H 191 " pdb=" C ARG H 191 " pdb=" N VAL H 192 " pdb=" CA VAL H 192 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA SER G 49 " pdb=" C SER G 49 " pdb=" N SER G 50 " pdb=" CA SER G 50 " ideal model delta harmonic sigma weight residual -180.00 -159.77 -20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C4' DA U 28 " pdb=" C3' DA U 28 " pdb=" O3' DA U 28 " pdb=" P DG U 29 " ideal model delta sinusoidal sigma weight residual -140.00 36.29 -176.29 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 19285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3465 0.038 - 0.076: 1051 0.076 - 0.114: 367 0.114 - 0.152: 71 0.152 - 0.190: 3 Chirality restraints: 4957 Sorted by residual: chirality pdb=" C3' DG U 47 " pdb=" C4' DG U 47 " pdb=" O3' DG U 47 " pdb=" C2' DG U 47 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.99e-01 chirality pdb=" C3' DC V 51 " pdb=" C4' DC V 51 " pdb=" O3' DC V 51 " pdb=" C2' DC V 51 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" C3' DC U 27 " pdb=" C4' DC U 27 " pdb=" O3' DC U 27 " pdb=" C2' DC U 27 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 4954 not shown) Planarity restraints: 5293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR I1115 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C THR I1115 " -0.032 2.00e-02 2.50e+03 pdb=" O THR I1115 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS I1116 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR I 896 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO I 897 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO I 897 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 897 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS I1116 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" C HIS I1116 " -0.029 2.00e-02 2.50e+03 pdb=" O HIS I1116 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU I1117 " 0.010 2.00e-02 2.50e+03 ... (remaining 5290 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 176 2.53 - 3.12: 22356 3.12 - 3.71: 46109 3.71 - 4.31: 63980 4.31 - 4.90: 109837 Nonbonded interactions: 242458 Sorted by model distance: nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 1.934 2.170 nonbonded pdb="MG MG J1501 " pdb=" O2A ATP J1504 " model vdw 2.001 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.036 2.170 nonbonded pdb="MG MG J1501 " pdb=" O HOH V 201 " model vdw 2.084 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.127 2.170 ... (remaining 242453 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 5.460 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 31.850 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.285 31748 Z= 0.246 Angle : 0.538 7.106 43367 Z= 0.368 Chirality : 0.042 0.190 4957 Planarity : 0.004 0.043 5293 Dihedral : 15.214 176.286 12456 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.44 % Allowed : 7.20 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3667 helix: 1.21 (0.15), residues: 1347 sheet: -0.05 (0.23), residues: 504 loop : -0.56 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I1246 TYR 0.011 0.001 TYR J 631 PHE 0.009 0.001 PHE M 133 TRP 0.007 0.001 TRP J 686 HIS 0.004 0.001 HIS M 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.23 (31740) covalent geometry : angle 0.53852 / 0.37 (43355) hydrogen bonds : bond 0.14021 / 9.37 ( 1329) hydrogen bonds : angle 5.58676 / 3.83 ( 3638) metal coordination : bond 0.17628 / 12.53 ( 8) metal coordination : angle 0.08321 / 0.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 211 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8386 (mt-10) REVERT: H 25 LYS cc_start: 0.8777 (ttmt) cc_final: 0.8423 (ttmm) REVERT: I 204 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8375 (mp) REVERT: I 283 LYS cc_start: 0.8822 (mttt) cc_final: 0.8545 (tppt) REVERT: I 370 MET cc_start: 0.8554 (mmm) cc_final: 0.8236 (mmm) REVERT: I 487 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7545 (pt) REVERT: I 488 MET cc_start: 0.8219 (tpt) cc_final: 0.7746 (tpt) REVERT: I 947 GLU cc_start: 0.8667 (tt0) cc_final: 0.8357 (tp30) REVERT: I 951 MET cc_start: 0.8924 (mtm) cc_final: 0.7887 (mtp) REVERT: I 1011 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7844 (mt) REVERT: I 1072 ASN cc_start: 0.9327 (OUTLIER) cc_final: 0.8901 (p0) REVERT: J 430 HIS cc_start: 0.8756 (OUTLIER) cc_final: 0.8512 (p90) REVERT: J 870 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8746 (t0) REVERT: J 962 ASN cc_start: 0.8317 (m-40) cc_final: 0.8116 (t0) REVERT: J 1192 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8606 (mttt) outliers start: 77 outliers final: 23 residues processed: 282 average time/residue: 0.1849 time to fit residues: 83.5737 Evaluate side-chains 172 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 67 GLU Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain J residue 176 PHE Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1049 GLN Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1192 LYS Chi-restraints excluded: chain K residue 18 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I1023 HIS J 266 ASN J1010 GLN M 282 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.079154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.052358 restraints weight = 92853.350| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.88 r_work: 0.2778 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31748 Z= 0.127 Angle : 0.525 7.958 43367 Z= 0.288 Chirality : 0.042 0.351 4957 Planarity : 0.004 0.066 5293 Dihedral : 16.246 175.566 5303 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.81 % Allowed : 9.08 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3667 helix: 1.41 (0.14), residues: 1396 sheet: 0.10 (0.24), residues: 482 loop : -0.49 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 976 TYR 0.011 0.001 TYR J 679 PHE 0.013 0.001 PHE J 7 TRP 0.020 0.001 TRP I 997 HIS 0.008 0.001 HIS M 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (31740) covalent geometry : angle 0.52309 / 0.29 (43355) hydrogen bonds : bond 0.04780 / 3.17 ( 1329) hydrogen bonds : angle 4.48291 / 3.05 ( 3638) metal coordination : bond 0.00970 / 0.69 ( 8) metal coordination : angle 2.77777 / 1.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 155 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8106 (mt-10) REVERT: H 25 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8134 (ttmm) REVERT: H 95 LYS cc_start: 0.8765 (ptmt) cc_final: 0.8526 (ptpp) REVERT: I 204 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8256 (mp) REVERT: I 283 LYS cc_start: 0.8889 (mttt) cc_final: 0.8599 (tppt) REVERT: I 487 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.6847 (pt) REVERT: I 488 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7346 (tpt) REVERT: I 947 GLU cc_start: 0.8865 (tt0) cc_final: 0.8421 (tp30) REVERT: I 951 MET cc_start: 0.8704 (mtm) cc_final: 0.8410 (mtp) REVERT: I 1011 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7777 (mt) REVERT: J 5 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8627 (mm) REVERT: J 227 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8466 (t80) REVERT: J 283 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.8991 (mm) REVERT: J 962 ASN cc_start: 0.8350 (m-40) cc_final: 0.8018 (t0) REVERT: J 1072 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7917 (mmtp) outliers start: 57 outliers final: 24 residues processed: 203 average time/residue: 0.1562 time to fit residues: 53.5692 Evaluate side-chains 172 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 193 GLU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1192 LYS Chi-restraints excluded: chain K residue 42 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 146 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 265 optimal weight: 0.0170 chunk 49 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 0.0070 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 132 HIS I 519 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.079641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.052881 restraints weight = 93114.265| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.90 r_work: 0.2794 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 31748 Z= 0.105 Angle : 0.485 7.757 43367 Z= 0.267 Chirality : 0.041 0.347 4957 Planarity : 0.004 0.066 5293 Dihedral : 16.245 175.586 5287 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.00 % Allowed : 9.36 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.14), residues: 3667 helix: 1.62 (0.14), residues: 1397 sheet: 0.26 (0.24), residues: 473 loop : -0.45 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 456 TYR 0.012 0.001 TYR J 679 PHE 0.010 0.001 PHE I 972 TRP 0.023 0.001 TRP I 997 HIS 0.004 0.000 HIS M 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.11 (31740) covalent geometry : angle 0.48357 / 0.27 (43355) hydrogen bonds : bond 0.03971 / 2.64 ( 1329) hydrogen bonds : angle 4.16881 / 2.84 ( 3638) metal coordination : bond 0.00596 / 0.44 ( 8) metal coordination : angle 2.21455 / 1.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 151 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: H 25 LYS cc_start: 0.8574 (ttmt) cc_final: 0.8115 (ttmm) REVERT: H 95 LYS cc_start: 0.8769 (ptmt) cc_final: 0.8518 (ptpt) REVERT: I 204 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8267 (mp) REVERT: I 487 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6926 (pt) REVERT: I 488 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7461 (tpt) REVERT: I 882 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9117 (mp) REVERT: I 947 GLU cc_start: 0.8840 (tt0) cc_final: 0.8384 (tp30) REVERT: I 951 MET cc_start: 0.8731 (mtm) cc_final: 0.8519 (mtp) REVERT: I 1011 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7825 (mt) REVERT: J 5 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8508 (mm) REVERT: J 227 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8453 (t80) REVERT: J 283 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.8966 (mm) REVERT: J 304 ASP cc_start: 0.8315 (m-30) cc_final: 0.8053 (m-30) REVERT: J 962 ASN cc_start: 0.8383 (m-40) cc_final: 0.8059 (t0) REVERT: J 1072 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7909 (mmtp) REVERT: K 79 GLU cc_start: 0.7756 (tp30) cc_final: 0.7533 (mm-30) REVERT: M 376 MET cc_start: 0.8145 (tpt) cc_final: 0.7934 (tpt) outliers start: 63 outliers final: 32 residues processed: 205 average time/residue: 0.1705 time to fit residues: 57.7752 Evaluate side-chains 179 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1192 LYS Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain M residue 209 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 273 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 288 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 269 optimal weight: 0.0980 chunk 296 optimal weight: 5.9990 chunk 311 optimal weight: 8.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 157 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 HIS K 73 GLN ** M 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.077344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.050336 restraints weight = 93588.609| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.89 r_work: 0.2728 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 31748 Z= 0.276 Angle : 0.596 8.644 43367 Z= 0.316 Chirality : 0.044 0.337 4957 Planarity : 0.004 0.085 5293 Dihedral : 16.364 175.383 5282 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.48 % Allowed : 10.41 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3667 helix: 1.47 (0.14), residues: 1399 sheet: 0.13 (0.24), residues: 488 loop : -0.56 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 994 TYR 0.013 0.001 TYR J 679 PHE 0.020 0.002 PHE I 230 TRP 0.046 0.002 TRP I 997 HIS 0.004 0.001 HIS M 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.28 (31740) covalent geometry : angle 0.59342 / 0.32 (43355) hydrogen bonds : bond 0.04948 / 3.29 ( 1329) hydrogen bonds : angle 4.35094 / 2.96 ( 3638) metal coordination : bond 0.01416 / 0.98 ( 8) metal coordination : angle 3.04833 / 1.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 136 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 76 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: I 204 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8313 (mp) REVERT: I 283 LYS cc_start: 0.8861 (mttt) cc_final: 0.8570 (tppt) REVERT: I 487 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6822 (pt) REVERT: I 488 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7535 (tpt) REVERT: I 542 ARG cc_start: 0.8040 (mtt-85) cc_final: 0.7711 (mtp85) REVERT: I 545 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: I 882 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9147 (mp) REVERT: I 947 GLU cc_start: 0.8836 (tt0) cc_final: 0.8419 (tp30) REVERT: I 951 MET cc_start: 0.8786 (mtm) cc_final: 0.8553 (mtm) REVERT: I 1304 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8755 (tpt) REVERT: J 5 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8607 (mm) REVERT: J 227 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8539 (t80) REVERT: J 962 ASN cc_start: 0.8576 (m-40) cc_final: 0.8247 (t0) REVERT: M 376 MET cc_start: 0.8125 (tpt) cc_final: 0.7889 (tpt) outliers start: 78 outliers final: 43 residues processed: 205 average time/residue: 0.1690 time to fit residues: 58.5977 Evaluate side-chains 184 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 132 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 937 ILE Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1192 LYS Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain M residue 209 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 255 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 323 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 159 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.079036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.051810 restraints weight = 93163.320| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.92 r_work: 0.2776 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31748 Z= 0.109 Angle : 0.491 8.809 43367 Z= 0.267 Chirality : 0.041 0.345 4957 Planarity : 0.004 0.095 5293 Dihedral : 16.329 175.578 5280 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.84 % Allowed : 11.33 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.14), residues: 3667 helix: 1.66 (0.14), residues: 1397 sheet: 0.21 (0.24), residues: 495 loop : -0.44 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 994 TYR 0.012 0.001 TYR J 679 PHE 0.023 0.001 PHE I 972 TRP 0.048 0.001 TRP I 997 HIS 0.003 0.000 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (31740) covalent geometry : angle 0.48964 / 0.27 (43355) hydrogen bonds : bond 0.03874 / 2.59 ( 1329) hydrogen bonds : angle 4.08610 / 2.78 ( 3638) metal coordination : bond 0.00437 / 0.32 ( 8) metal coordination : angle 2.32856 / 1.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 143 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: H 212 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7289 (t0) REVERT: I 204 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8316 (mp) REVERT: I 488 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7457 (tpt) REVERT: I 745 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8265 (pt0) REVERT: I 882 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9101 (mp) REVERT: I 947 GLU cc_start: 0.8819 (tt0) cc_final: 0.8371 (tp30) REVERT: I 951 MET cc_start: 0.8797 (mtm) cc_final: 0.8541 (mtm) REVERT: J 5 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8525 (mm) REVERT: J 227 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8446 (t80) REVERT: J 283 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.8962 (mm) REVERT: J 821 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8174 (tmm) REVERT: J 962 ASN cc_start: 0.8547 (m-40) cc_final: 0.8234 (t0) outliers start: 58 outliers final: 38 residues processed: 192 average time/residue: 0.1705 time to fit residues: 55.5227 Evaluate side-chains 182 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 134 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1192 LYS Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain M residue 209 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 355 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 280 optimal weight: 5.9990 chunk 311 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 308 optimal weight: 5.9990 chunk 255 optimal weight: 0.1980 chunk 15 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN ** J 320 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 = 0.3554 r_free = 0.3554 target = 0.077911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.050796 restraints weight = 94086.351| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.92 r_work: 0.2745 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 31748 Z= 0.195 Angle : 0.533 7.766 43367 Z= 0.284 Chirality : 0.042 0.340 4957 Planarity : 0.004 0.098 5293 Dihedral : 16.375 175.451 5277 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.44 % Allowed : 11.42 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.14), residues: 3667 helix: 1.66 (0.14), residues: 1394 sheet: 0.20 (0.24), residues: 488 loop : -0.48 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 974 TYR 0.013 0.001 TYR J 679 PHE 0.023 0.001 PHE I 972 TRP 0.055 0.002 TRP I 997 HIS 0.003 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (31740) covalent geometry : angle 0.53082 / 0.28 (43355) hydrogen bonds : bond 0.04285 / 2.86 ( 1329) hydrogen bonds : angle 4.14830 / 2.81 ( 3638) metal coordination : bond 0.01028 / 0.72 ( 8) metal coordination : angle 2.61435 / 1.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 136 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8107 (mt-10) REVERT: I 204 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8332 (mp) REVERT: I 275 ARG cc_start: 0.8303 (mtt90) cc_final: 0.7941 (tpm170) REVERT: I 487 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.6823 (pt) REVERT: I 488 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7558 (tpt) REVERT: I 542 ARG cc_start: 0.8086 (mtt-85) cc_final: 0.7704 (mtp85) REVERT: I 697 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8772 (pttm) REVERT: I 745 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8286 (pt0) REVERT: I 882 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9106 (mp) REVERT: I 947 GLU cc_start: 0.8820 (tt0) cc_final: 0.8384 (tp30) REVERT: I 951 MET cc_start: 0.8815 (mtm) cc_final: 0.8563 (mtm) REVERT: J 5 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8550 (mm) REVERT: J 227 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.8489 (t80) REVERT: J 283 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.8979 (mm) REVERT: J 304 ASP cc_start: 0.8343 (m-30) cc_final: 0.8116 (m-30) REVERT: J 321 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7481 (mttp) REVERT: J 821 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8210 (tmm) REVERT: J 962 ASN cc_start: 0.8648 (m-40) cc_final: 0.8350 (t0) outliers start: 77 outliers final: 52 residues processed: 204 average time/residue: 0.1661 time to fit residues: 57.3373 Evaluate side-chains 195 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 132 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 994 ARG Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 937 ILE Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1192 LYS Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain M residue 209 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 321 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 341 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 268 optimal weight: 0.9980 chunk 358 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 267 optimal weight: 2.9990 chunk 194 optimal weight: 0.0970 chunk 101 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.079185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.052293 restraints weight = 92091.479| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.87 r_work: 0.2783 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31748 Z= 0.106 Angle : 0.481 9.023 43367 Z= 0.261 Chirality : 0.041 0.345 4957 Planarity : 0.004 0.091 5293 Dihedral : 16.363 175.612 5277 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.16 % Allowed : 11.84 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.14), residues: 3667 helix: 1.77 (0.14), residues: 1398 sheet: 0.21 (0.24), residues: 497 loop : -0.39 (0.15), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 974 TYR 0.012 0.001 TYR J 679 PHE 0.017 0.001 PHE I 972 TRP 0.085 0.002 TRP I 997 HIS 0.003 0.000 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (31740) covalent geometry : angle 0.48009 / 0.26 (43355) hydrogen bonds : bond 0.03587 / 2.40 ( 1329) hydrogen bonds : angle 3.97715 / 2.70 ( 3638) metal coordination : bond 0.00498 / 0.36 ( 8) metal coordination : angle 2.24694 / 1.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 139 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: I 204 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8345 (mp) REVERT: I 487 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.6813 (pt) REVERT: I 488 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7456 (tpt) REVERT: I 542 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7787 (mtp85) REVERT: I 745 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8313 (pt0) REVERT: I 882 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.9086 (mp) REVERT: I 947 GLU cc_start: 0.8809 (tt0) cc_final: 0.8372 (tp30) REVERT: I 951 MET cc_start: 0.8807 (mtm) cc_final: 0.8535 (mtm) REVERT: J 5 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8493 (mm) REVERT: J 227 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8482 (t80) REVERT: J 264 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8299 (p0) REVERT: J 283 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.8946 (mm) REVERT: J 304 ASP cc_start: 0.8294 (m-30) cc_final: 0.8059 (m-30) REVERT: J 321 LYS cc_start: 0.8083 (mmtt) cc_final: 0.7499 (mttp) REVERT: J 821 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8339 (tmm) REVERT: J 962 ASN cc_start: 0.8585 (m-40) cc_final: 0.8267 (t0) REVERT: J 1189 MET cc_start: 0.8548 (mmm) cc_final: 0.8251 (tpt) REVERT: M 108 GLU cc_start: 0.6527 (tt0) cc_final: 0.6319 (tt0) outliers start: 68 outliers final: 45 residues processed: 200 average time/residue: 0.1766 time to fit residues: 60.1890 Evaluate side-chains 191 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 135 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 994 ARG Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1192 LYS Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain M residue 209 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 237 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 245 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 185 optimal weight: 9.9990 chunk 321 optimal weight: 6.9990 chunk 273 optimal weight: 5.9990 chunk 301 optimal weight: 10.0000 chunk 346 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 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 = 0.3571 r_free = 0.3571 target = 0.078673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.051556 restraints weight = 92665.868| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.88 r_work: 0.2772 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31748 Z= 0.142 Angle : 0.495 8.173 43367 Z= 0.266 Chirality : 0.041 0.342 4957 Planarity : 0.004 0.085 5293 Dihedral : 16.392 175.586 5276 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.19 % Allowed : 11.90 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.14), residues: 3667 helix: 1.74 (0.14), residues: 1401 sheet: 0.18 (0.24), residues: 497 loop : -0.38 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 974 TYR 0.013 0.001 TYR J 679 PHE 0.025 0.001 PHE I 972 TRP 0.067 0.001 TRP I 997 HIS 0.003 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (31740) covalent geometry : angle 0.49374 / 0.27 (43355) hydrogen bonds : bond 0.03792 / 2.53 ( 1329) hydrogen bonds : angle 3.99794 / 2.71 ( 3638) metal coordination : bond 0.00738 / 0.52 ( 8) metal coordination : angle 2.39614 / 1.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 140 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8093 (mt-10) REVERT: I 204 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8372 (mp) REVERT: I 275 ARG cc_start: 0.8333 (mtt90) cc_final: 0.7957 (tpm170) REVERT: I 487 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.6806 (pt) REVERT: I 488 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7465 (tpt) REVERT: I 542 ARG cc_start: 0.8109 (mtt-85) cc_final: 0.7686 (mtp85) REVERT: I 697 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8720 (pttm) REVERT: I 745 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8314 (pt0) REVERT: I 882 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.9083 (mp) REVERT: I 947 GLU cc_start: 0.8794 (tt0) cc_final: 0.8372 (tp30) REVERT: I 951 MET cc_start: 0.8798 (mtm) cc_final: 0.8533 (mtm) REVERT: I 1304 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8692 (tpt) REVERT: J 5 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8505 (mm) REVERT: J 227 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8497 (t80) REVERT: J 283 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8969 (mm) REVERT: J 304 ASP cc_start: 0.8292 (m-30) cc_final: 0.8053 (m-30) REVERT: J 321 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7538 (mttp) REVERT: J 821 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8327 (tmm) REVERT: J 962 ASN cc_start: 0.8600 (m-40) cc_final: 0.8273 (t0) outliers start: 69 outliers final: 49 residues processed: 198 average time/residue: 0.1831 time to fit residues: 60.9768 Evaluate side-chains 196 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 135 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 994 ARG Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 937 ILE Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1192 LYS Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain M residue 209 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 119 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 321 optimal weight: 6.9990 chunk 303 optimal weight: 2.9990 chunk 272 optimal weight: 0.4980 chunk 293 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1111 GLN ** J 320 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 = 0.3560 r_free = 0.3560 target = 0.078271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.051610 restraints weight = 93888.846| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.88 r_work: 0.2752 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31748 Z= 0.174 Angle : 0.517 9.061 43367 Z= 0.276 Chirality : 0.042 0.342 4957 Planarity : 0.004 0.075 5293 Dihedral : 16.452 175.733 5276 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.13 % Allowed : 12.03 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.14), residues: 3667 helix: 1.69 (0.14), residues: 1404 sheet: 0.26 (0.24), residues: 483 loop : -0.41 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 974 TYR 0.012 0.001 TYR J 679 PHE 0.019 0.001 PHE I 972 TRP 0.077 0.002 TRP I 997 HIS 0.003 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (31740) covalent geometry : angle 0.51545 / 0.28 (43355) hydrogen bonds : bond 0.04020 / 2.68 ( 1329) hydrogen bonds : angle 4.04841 / 2.74 ( 3638) metal coordination : bond 0.00880 / 0.61 ( 8) metal coordination : angle 2.54922 / 1.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 136 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: I 204 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8370 (mp) REVERT: I 275 ARG cc_start: 0.8306 (mtt90) cc_final: 0.7956 (tpm170) REVERT: I 487 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6731 (pt) REVERT: I 488 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7514 (tpt) REVERT: I 542 ARG cc_start: 0.8065 (mtt-85) cc_final: 0.7641 (mtp85) REVERT: I 697 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8765 (pttm) REVERT: I 745 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: I 882 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9085 (mp) REVERT: I 947 GLU cc_start: 0.8805 (tt0) cc_final: 0.8389 (tp30) REVERT: I 951 MET cc_start: 0.8822 (mtm) cc_final: 0.8547 (mtm) REVERT: I 1304 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8705 (tpt) REVERT: J 5 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8496 (mm) REVERT: J 227 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8555 (t80) REVERT: J 283 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8964 (mm) REVERT: J 304 ASP cc_start: 0.8304 (m-30) cc_final: 0.8077 (m-30) REVERT: J 321 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7564 (mttp) REVERT: J 821 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8360 (tmm) REVERT: J 962 ASN cc_start: 0.8642 (m-40) cc_final: 0.8331 (t0) REVERT: J 1189 MET cc_start: 0.8563 (mmm) cc_final: 0.8295 (tpt) REVERT: K 79 GLU cc_start: 0.7918 (tp30) cc_final: 0.7671 (mm-30) outliers start: 67 outliers final: 52 residues processed: 194 average time/residue: 0.1661 time to fit residues: 54.3897 Evaluate side-chains 198 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 134 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 994 ARG Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 937 ILE Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1011 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1192 LYS Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 452 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 274 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 315 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 288 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 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 = 0.3545 r_free = 0.3545 target = 0.077461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.050324 restraints weight = 94350.325| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.91 r_work: 0.2738 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 31748 Z= 0.218 Angle : 0.552 8.723 43367 Z= 0.292 Chirality : 0.043 0.340 4957 Planarity : 0.004 0.084 5293 Dihedral : 16.512 175.859 5276 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.13 % Allowed : 12.09 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3667 helix: 1.60 (0.14), residues: 1403 sheet: 0.20 (0.24), residues: 483 loop : -0.45 (0.15), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 974 TYR 0.013 0.001 TYR J 679 PHE 0.023 0.001 PHE I 972 TRP 0.079 0.002 TRP I 997 HIS 0.003 0.001 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (31740) covalent geometry : angle 0.54970 / 0.29 (43355) hydrogen bonds : bond 0.04331 / 2.89 ( 1329) hydrogen bonds : angle 4.13701 / 2.80 ( 3638) metal coordination : bond 0.01078 / 0.75 ( 8) metal coordination : angle 2.73349 / 1.52 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7334 Ramachandran restraints generated. 3667 Oldfield, 0 Emsley, 3667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 131 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: I 204 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8375 (mp) REVERT: I 275 ARG cc_start: 0.8299 (mtt90) cc_final: 0.7939 (tpm170) REVERT: I 487 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6739 (pt) REVERT: I 488 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7519 (tpt) REVERT: I 542 ARG cc_start: 0.8060 (mtt-85) cc_final: 0.7642 (mtp85) REVERT: I 697 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8822 (pttm) REVERT: I 745 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8322 (pt0) REVERT: I 882 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9105 (mp) REVERT: I 947 GLU cc_start: 0.8804 (tt0) cc_final: 0.8391 (tp30) REVERT: I 951 MET cc_start: 0.8835 (mtm) cc_final: 0.8576 (mtm) REVERT: I 1304 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8720 (tpt) REVERT: J 5 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8514 (mm) REVERT: J 227 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8616 (t80) REVERT: J 279 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8913 (tm) REVERT: J 283 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.8955 (mm) REVERT: J 321 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7578 (mttp) REVERT: J 821 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8348 (tmm) REVERT: J 962 ASN cc_start: 0.8672 (m-40) cc_final: 0.8348 (t0) REVERT: J 1189 MET cc_start: 0.8556 (mmm) cc_final: 0.8291 (tpt) outliers start: 67 outliers final: 51 residues processed: 189 average time/residue: 0.1627 time to fit residues: 52.3526 Evaluate side-chains 194 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 130 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 62 TYR Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 488 MET Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 745 GLU Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 994 ARG Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 204 GLU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 283 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 790 THR Chi-restraints excluded: chain J residue 821 MET Chi-restraints excluded: chain J residue 856 ILE Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 937 ILE Chi-restraints excluded: chain J residue 966 VAL Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1162 ILE Chi-restraints excluded: chain J residue 1192 LYS Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 452 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 53 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 291 optimal weight: 5.9990 chunk 308 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 356 optimal weight: 7.9990 chunk 133 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 207 optimal weight: 0.2980 chunk 263 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.078574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.051752 restraints weight = 94045.073| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.92 r_work: 0.2760 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31748 Z= 0.121 Angle : 0.498 9.483 43367 Z= 0.268 Chirality : 0.041 0.346 4957 Planarity : 0.004 0.080 5293 Dihedral : 16.490 176.001 5276 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.94 % Allowed : 12.35 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3667 helix: 1.68 (0.14), residues: 1405 sheet: 0.19 (0.24), residues: 491 loop : -0.37 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 974 TYR 0.012 0.001 TYR J 679 PHE 0.019 0.001 PHE I 972 TRP 0.078 0.002 TRP I 997 HIS 0.003 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (31740) covalent geometry : angle 0.49637 / 0.27 (43355) hydrogen bonds : bond 0.03735 / 2.49 ( 1329) hydrogen bonds : angle 4.00784 / 2.72 ( 3638) metal coordination : bond 0.00589 / 0.42 ( 8) metal coordination : angle 2.41497 / 1.35 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6897.41 seconds wall clock time: 118 minutes 41.00 seconds (7121.00 seconds total)