Starting phenix.real_space_refine on Sun Aug 9 06:23:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ymu_73122/08_2026/9ymu_73122.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ymu_73122/08_2026/9ymu_73122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ymu_73122/08_2026/9ymu_73122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ymu_73122/08_2026/9ymu_73122.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ymu_73122/08_2026/9ymu_73122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ymu_73122/08_2026/9ymu_73122.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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 121 5.49 5 Mg 2 5.21 5 S 129 5.16 5 C 19352 2.51 5 N 5578 2.21 5 O 7112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32296 Number of models: 1 Model: "" Number of chains: 19 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "J" Number of atoms: 10555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1360, 10555 Classifications: {'peptide': 1360} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1304} Chain: "K" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 610 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "P" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1259 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 1} Chain: "G" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1748 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 216} Chain breaks: 1 Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1710 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "L" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3837 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 15, 'TRANS': 455} Chain breaks: 2 Chain: "Q" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1116 Classifications: {'DNA': 55} Link IDs: {'rna3p': 54} Chain breaks: 1 Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 33 Unusual residues: {' MG': 2, ' ZN': 2, 'CTP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 290 Classifications: {'water': 290} Link IDs: {None: 289} Chain: "J" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 281 Classifications: {'water': 281} Link IDs: {None: 280} Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "P" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "R" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "L" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 91 Classifications: {'water': 91} Link IDs: {None: 90} Chain: "Q" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11016 SG CYS J 70 50.379 53.762 116.391 1.00 72.66 S ATOM 11030 SG CYS J 72 52.607 52.637 119.192 1.00 74.02 S ATOM 11138 SG CYS J 85 48.960 53.039 119.846 1.00 71.03 S ATOM 11162 SG CYS J 88 51.157 56.068 119.315 1.00 70.47 S ATOM 16850 SG CYS J 814 22.546 109.153 85.985 1.00 36.43 S ATOM 17415 SG CYS J 888 25.889 107.800 87.093 1.00 24.84 S ATOM 17466 SG CYS J 895 24.300 106.537 83.991 1.00 27.37 S ATOM 17487 SG CYS J 898 25.679 109.986 84.041 1.00 33.09 S Time building chain proxies: 6.48, per 1000 atoms: 0.20 Number of scatterers: 32296 At special positions: 0 Unit cell: (153.94, 177.16, 193.5, 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 129 16.00 P 121 15.00 Mg 2 11.99 O 7112 8.00 N 5578 7.00 C 19352 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: 2.58 Conformation dependent library (CDL) restraints added in 1.0 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 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 12 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6854 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 48 sheets defined 44.5% alpha, 16.7% beta 48 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.676A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 4.022A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.744A 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: 4.126A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.519A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 293 Processing helix chain 'I' and resid 318 through 327 removed outlier: 3.607A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 4.078A pdb=" N GLU I 382 " --> pdb=" O ARG I 378 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 409 Processing helix chain 'I' and resid 421 through 438 removed outlier: 3.534A pdb=" N ILE I 425 " --> pdb=" O SER I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.692A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 493 removed outlier: 3.862A pdb=" N MET I 492 " --> pdb=" O MET I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 509 removed outlier: 3.601A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL I 502 " --> pdb=" O ILE I 498 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 539 through 543 Processing helix chain 'I' and resid 551 through 555 Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.922A 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 664 through 668 removed outlier: 3.595A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 removed outlier: 4.028A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 713 removed outlier: 4.177A pdb=" N GLY I 713 " --> pdb=" O ALA I 709 " (cutoff:3.500A) Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 859 through 863 Processing helix chain 'I' and resid 896 through 907 Processing helix chain 'I' and resid 942 through 981 removed outlier: 3.550A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) Processing helix chain 'I' and resid 987 through 992 Processing helix chain 'I' and resid 993 through 999 removed outlier: 4.240A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1009 removed outlier: 3.833A pdb=" N ASN I1009 " --> pdb=" O GLU I1006 " (cutoff:3.500A) Processing helix chain 'I' and resid 1010 through 1038 Processing helix chain 'I' and resid 1081 through 1085 removed outlier: 3.671A pdb=" N MET I1085 " --> pdb=" O ILE I1082 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1107 removed outlier: 4.216A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.560A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.571A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.721A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1283 through 1292 Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.703A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.808A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 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: 3.933A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG J 98 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 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 173 Processing helix chain 'J' and resid 180 through 191 removed outlier: 3.850A pdb=" N ALA J 184 " --> pdb=" O MET J 180 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 207 Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.573A pdb=" N ARG J 214 " --> pdb=" O SER J 210 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS J 215 " --> pdb=" O GLU J 211 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS J 216 " --> pdb=" O THR J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 264 through 286 removed outlier: 3.622A pdb=" N LEU J 268 " --> pdb=" O ASP J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.596A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.944A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 613 through 636 removed outlier: 3.735A pdb=" N THR J 617 " --> pdb=" O GLY J 613 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP J 622 " --> pdb=" O VAL J 618 " (cutoff:3.500A) removed outlier: 3.773A 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 729 removed outlier: 3.514A pdb=" N GLY J 729 " --> pdb=" O MET J 725 " (cutoff:3.500A) Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.941A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG J 738 " --> pdb=" O ALA J 734 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN J 739 " --> pdb=" O ALA J 735 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU J 740 " --> pdb=" O GLN J 736 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA J 741 " --> pdb=" O ILE J 737 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 789 removed outlier: 4.070A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR J 786 " --> pdb=" O GLY J 782 " (cutoff:3.500A) Processing helix chain 'J' and resid 789 through 805 removed outlier: 4.188A pdb=" N SER J 793 " --> pdb=" O LYS J 789 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 932 removed outlier: 3.602A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Proline residue: J 926 - end of helix removed outlier: 3.511A pdb=" N MET J 932 " --> pdb=" O THR J 928 " (cutoff:3.500A) Processing helix chain 'J' and resid 1069 through 1073 removed outlier: 4.078A pdb=" N ASP J1073 " --> pdb=" O GLY J1070 " (cutoff:3.500A) Processing helix chain 'J' and resid 1133 through 1146 Proline residue: J1139 - end of helix Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.510A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR J1241 " --> pdb=" O VAL J1237 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1260 removed outlier: 4.346A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1326 Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1353 removed outlier: 3.568A 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 1375 removed outlier: 3.736A pdb=" N MET J1370 " --> pdb=" O HIS J1366 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG J1371 " --> pdb=" O GLN J1367 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 32 removed outlier: 3.624A pdb=" N VAL K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN K 29 " --> pdb=" O ARG K 25 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET K 30 " --> pdb=" O ARG K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 78 Processing helix chain 'G' and resid 34 through 48 removed outlier: 3.760A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 158 removed outlier: 3.602A pdb=" N ARG G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 228 Processing helix chain 'G' and resid 228 through 233 removed outlier: 3.868A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.991A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.678A 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 227 Processing helix chain 'L' and resid 96 through 106 Processing helix chain 'L' and resid 112 through 134 Processing helix chain 'L' and resid 137 through 153 removed outlier: 3.872A pdb=" N ILE L 141 " --> pdb=" O TYR L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 215 through 234 removed outlier: 3.600A pdb=" N THR L 234 " --> pdb=" O VAL L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 259 Processing helix chain 'L' and resid 262 through 296 removed outlier: 3.809A pdb=" N GLU L 293 " --> pdb=" O LYS L 289 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN L 294 " --> pdb=" O LEU L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 307 Processing helix chain 'L' and resid 313 through 320 Processing helix chain 'L' and resid 324 through 330 Processing helix chain 'L' and resid 333 through 352 Processing helix chain 'L' and resid 354 through 383 removed outlier: 3.547A pdb=" N ALA L 382 " --> pdb=" O GLU L 378 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN L 383 " --> pdb=" O MET L 379 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 393 removed outlier: 4.119A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE L 388 " --> pdb=" O LEU L 384 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 418 removed outlier: 3.595A pdb=" N ILE L 410 " --> pdb=" O GLN L 406 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY L 411 " --> pdb=" O GLU L 407 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 424 removed outlier: 3.858A pdb=" N ARG L 423 " --> pdb=" O GLU L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 447 removed outlier: 3.944A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 Processing helix chain 'L' and resid 479 through 488 removed outlier: 3.867A pdb=" N GLU L 485 " --> pdb=" O GLU L 481 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG L 486 " --> pdb=" O GLU L 482 " (cutoff:3.500A) Processing helix chain 'L' and resid 490 through 498 Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.595A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 549 Processing helix chain 'L' and resid 552 through 564 Processing helix chain 'L' and resid 572 through 580 removed outlier: 3.844A pdb=" N LYS L 578 " --> pdb=" O GLU L 574 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 599 Processing helix chain 'L' and resid 604 through 611 removed outlier: 3.711A pdb=" N SER L 609 " --> pdb=" O GLU L 605 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE L 610 " --> pdb=" O VAL L 606 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.543A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.816A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA I 94 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY I 125 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU I 96 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR I 123 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL I 98 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU I 121 " --> pdb=" O VAL I 98 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU I 100 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLU I 119 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 136 through 138 Processing sheet with id=AA4, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.605A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.588A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 284 through 287 removed outlier: 4.079A pdb=" N LEU I 237 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.597A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.328A pdb=" N ASP I 303 " --> pdb=" O LEU I 309 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU I 309 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 580 through 581 removed outlier: 7.182A pdb=" N LEU I 587 " --> pdb=" O LEU I 606 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU I 606 " --> pdb=" O LEU I 587 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR I 589 " --> pdb=" O HIS I 604 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N HIS I 604 " --> pdb=" O THR I 589 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR I 591 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU I 602 " --> pdb=" O TYR I 591 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS I 593 " --> pdb=" O THR I 600 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AB2, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.516A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.104A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AB5, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AB6, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.098A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.762A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.717A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 887 through 889 Processing sheet with id=AC1, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AC2, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.783A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.665A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.596A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.867A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 252 through 254 removed outlier: 6.518A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AC8, first strand: chain 'J' and resid 703 through 707 Processing sheet with id=AC9, first strand: chain 'J' and resid 745 through 748 removed outlier: 6.469A pdb=" N MET J 747 " --> pdb=" O THR J 757 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N THR J 757 " --> pdb=" O MET J 747 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AD2, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AD3, first strand: chain 'J' and resid 825 through 827 removed outlier: 6.742A pdb=" N GLU J 827 " --> pdb=" O VAL J 831 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL J 831 " --> pdb=" O GLU J 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.800A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 949 through 952 removed outlier: 6.633A pdb=" N ILE J 950 " --> pdb=" O VAL J1017 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU J1015 " --> pdb=" O VAL J 952 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 991 through 997 removed outlier: 3.738A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 4.149A pdb=" N ALA J1122 " --> pdb=" O VAL J1027 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 1077 through 1081 Processing sheet with id=AD9, first strand: chain 'J' and resid 1155 through 1156 removed outlier: 6.457A pdb=" N ILE J1155 " --> pdb=" O ILE J1210 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 1186 through 1191 Processing sheet with id=AE2, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.655A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 12 through 18 removed outlier: 5.012A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.790A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AE6, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.530A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 152 through 153 Processing sheet with id=AE8, first strand: chain 'H' and resid 13 through 18 removed outlier: 6.400A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASP H 197 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA H 190 " --> pdb=" O ASP H 197 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP H 199 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU H 188 " --> pdb=" O ASP H 199 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU H 201 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN H 186 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE H 203 " --> pdb=" O ALA H 184 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA H 184 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N MET H 205 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG H 182 " --> pdb=" O MET H 205 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR H 207 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL H 180 " --> pdb=" O THR H 207 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 97 through 105 removed outlier: 6.796A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AF2, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AF3, first strand: chain 'H' and resid 152 through 153 1338 hydrogen bonds defined for protein. 3768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 117 hydrogen bonds 234 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 10.09 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9174 1.33 - 1.45: 4924 1.45 - 1.57: 17626 1.57 - 1.69: 237 1.69 - 1.81: 227 Bond restraints: 32188 Sorted by residual: bond pdb=" O3B CTP J1505 " pdb=" PG CTP J1505 " ideal model delta sigma weight residual 1.751 1.608 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" C3' DC P 61 " pdb=" C2' DC P 61 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DC Q 23 " pdb=" C2' DC Q 23 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DG P 71 " pdb=" C2' DG P 71 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.61e+00 bond pdb=" C3' DA P 29 " pdb=" C2' DA P 29 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.49e+00 ... (remaining 32183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 43257 1.85 - 3.71: 658 3.71 - 5.56: 36 5.56 - 7.41: 6 7.41 - 9.27: 4 Bond angle restraints: 43961 Sorted by residual: angle pdb=" O4' DG P 63 " pdb=" C1' DG P 63 " pdb=" N9 DG P 63 " ideal model delta sigma weight residual 108.00 111.76 -3.76 7.00e-01 2.04e+00 2.88e+01 angle pdb=" N3 DT Q 14 " pdb=" C4 DT Q 14 " pdb=" O4 DT Q 14 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT P 31 " pdb=" C4 DT P 31 " pdb=" O4 DT P 31 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT P 28 " pdb=" C4 DT P 28 " pdb=" O4 DT P 28 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT Q 26 " pdb=" C4 DT Q 26 " pdb=" O4 DT Q 26 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 ... (remaining 43956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 18836 34.82 - 69.65: 703 69.65 - 104.47: 13 104.47 - 139.29: 0 139.29 - 174.11: 2 Dihedral angle restraints: 19554 sinusoidal: 8918 harmonic: 10636 Sorted by residual: dihedral pdb=" CA VAL H 192 " pdb=" C VAL H 192 " pdb=" N GLU H 193 " pdb=" CA GLU H 193 " ideal model delta harmonic sigma weight residual -180.00 -154.80 -25.20 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA SER I1295 " pdb=" C SER I1295 " pdb=" N ASP I1296 " pdb=" CA ASP I1296 " ideal model delta harmonic sigma weight residual -180.00 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 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 180.00 159.54 20.46 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 19551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3351 0.036 - 0.072: 1140 0.072 - 0.108: 398 0.108 - 0.144: 117 0.144 - 0.180: 5 Chirality restraints: 5011 Sorted by residual: chirality pdb=" C1' CTP J1505 " pdb=" C2' CTP J1505 " pdb=" N1 CTP J1505 " pdb=" O4' CTP J1505 " both_signs ideal model delta sigma weight residual False 2.35 2.53 -0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" C3' CTP J1505 " pdb=" C2' CTP J1505 " pdb=" C4' CTP J1505 " pdb=" O3' CTP J1505 " both_signs ideal model delta sigma weight residual False -2.71 -2.54 -0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CA GLU I 813 " pdb=" N GLU I 813 " pdb=" C GLU I 813 " pdb=" CB GLU I 813 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 5008 not shown) Planarity restraints: 5327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' CTP J1505 " 0.039 2.00e-02 2.50e+03 3.85e-02 3.34e+01 pdb=" C2 CTP J1505 " -0.004 2.00e-02 2.50e+03 pdb=" C4 CTP J1505 " 0.014 2.00e-02 2.50e+03 pdb=" C5 CTP J1505 " 0.046 2.00e-02 2.50e+03 pdb=" C6 CTP J1505 " -0.093 2.00e-02 2.50e+03 pdb=" N1 CTP J1505 " 0.022 2.00e-02 2.50e+03 pdb=" N3 CTP J1505 " -0.015 2.00e-02 2.50e+03 pdb=" N4 CTP J1505 " 0.005 2.00e-02 2.50e+03 pdb=" O2 CTP J1505 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR I 589 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO I 590 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO I 590 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 590 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG P 63 " -0.024 2.00e-02 2.50e+03 1.02e-02 3.13e+00 pdb=" N9 DG P 63 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DG P 63 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG P 63 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG P 63 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG P 63 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG P 63 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG P 63 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG P 63 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG P 63 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DG P 63 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG P 63 " 0.003 2.00e-02 2.50e+03 ... (remaining 5324 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 233 2.48 - 3.09: 20948 3.09 - 3.69: 47129 3.69 - 4.30: 74220 4.30 - 4.90: 121725 Nonbonded interactions: 264255 Sorted by model distance: nonbonded pdb="MG MG J1504 " pdb=" O2B CTP J1505 " model vdw 1.877 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 1.948 2.170 nonbonded pdb="MG MG J1504 " pdb=" O1A CTP J1505 " model vdw 2.030 2.170 nonbonded pdb="MG MG J1504 " pdb=" O2G CTP J1505 " model vdw 2.045 2.170 nonbonded pdb=" OD2 ASP J 460 " pdb="MG MG J1504 " model vdw 2.173 2.170 ... (remaining 264250 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 4 through 158 or resid 167 through 233)) selection = chain 'H' } 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: 5.300 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: 0.050 Extract box with map and model: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 38.110 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 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 0.143 32196 Z= 0.242 Angle : 0.542 9.266 43973 Z= 0.367 Chirality : 0.043 0.180 5011 Planarity : 0.004 0.047 5327 Dihedral : 15.152 174.114 12700 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.68 % Allowed : 6.11 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 3676 helix: 1.57 (0.14), residues: 1446 sheet: 0.54 (0.24), residues: 499 loop : -0.54 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I1246 TYR 0.014 0.001 TYR J 631 PHE 0.012 0.001 PHE I 514 TRP 0.006 0.001 TRP L 326 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.24 (32188) covalent geometry : angle 0.54159 / 0.37 (43961) hydrogen bonds : bond 0.13691 / 9.13 ( 1453) hydrogen bonds : angle 5.28462 / 3.72 ( 4002) metal coordination : bond 0.04517 / 1.86 ( 8) metal coordination : angle 0.03351 / 0.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 382 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 240 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8453 (tp30) REVERT: I 481 LEU cc_start: 0.8522 (pp) cc_final: 0.8150 (pp) REVERT: I 903 ARG cc_start: 0.8627 (mmt90) cc_final: 0.8367 (mtt-85) REVERT: J 873 GLU cc_start: 0.8546 (tp30) cc_final: 0.8345 (tp30) REVERT: J 1062 LEU cc_start: 0.9392 (mt) cc_final: 0.9144 (mt) REVERT: J 1063 ASP cc_start: 0.8424 (t0) cc_final: 0.7770 (t0) REVERT: K 73 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8445 (mm110) REVERT: G 233 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8143 (p0) REVERT: L 486 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8131 (mmm160) outliers start: 53 outliers final: 14 residues processed: 426 average time/residue: 0.8785 time to fit residues: 428.7800 Evaluate side-chains 257 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 241 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain L residue 486 ARG Chi-restraints excluded: chain L residue 527 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 667 GLN G 147 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN H 186 ASN ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.100619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.059101 restraints weight = 61167.932| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.51 r_work: 0.2554 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2413 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 32196 Z= 0.161 Angle : 0.565 8.594 43973 Z= 0.309 Chirality : 0.043 0.261 5011 Planarity : 0.005 0.096 5327 Dihedral : 16.365 175.861 5422 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.77 % Allowed : 11.40 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.14), residues: 3676 helix: 1.75 (0.14), residues: 1476 sheet: 0.68 (0.24), residues: 484 loop : -0.50 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 332 TYR 0.017 0.001 TYR H 68 PHE 0.020 0.001 PHE J1274 TRP 0.013 0.001 TRP L 326 HIS 0.007 0.001 HIS L 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (32188) covalent geometry : angle 0.56338 / 0.31 (43961) hydrogen bonds : bond 0.04741 / 3.15 ( 1453) hydrogen bonds : angle 4.38555 / 3.06 ( 4002) metal coordination : bond 0.00591 / 0.26 ( 8) metal coordination : angle 2.68413 / 1.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 270 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 240 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8481 (tp30) REVERT: I 244 GLU cc_start: 0.8988 (mp0) cc_final: 0.8749 (mp0) REVERT: I 272 ARG cc_start: 0.9065 (mmm160) cc_final: 0.8826 (mmp80) REVERT: I 315 MET cc_start: 0.8856 (ttp) cc_final: 0.8135 (mtm) REVERT: I 369 MET cc_start: 0.8766 (tmm) cc_final: 0.8556 (tmm) REVERT: I 899 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7912 (tm-30) REVERT: I 1127 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8390 (mptm) REVERT: J 177 ASP cc_start: 0.8716 (t0) cc_final: 0.7876 (p0) REVERT: J 827 GLU cc_start: 0.8761 (pt0) cc_final: 0.8253 (pp20) REVERT: J 844 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.9083 (p) REVERT: J 873 GLU cc_start: 0.9113 (tp30) cc_final: 0.8726 (tp30) REVERT: J 1063 ASP cc_start: 0.8621 (t0) cc_final: 0.8414 (t0) REVERT: J 1086 ASN cc_start: 0.9187 (t0) cc_final: 0.8874 (m110) REVERT: J 1143 ASP cc_start: 0.8618 (m-30) cc_final: 0.8392 (m-30) REVERT: J 1188 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8500 (tm-30) REVERT: J 1189 MET cc_start: 0.8978 (mmp) cc_final: 0.8605 (mmm) REVERT: J 1195 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7358 (tm-30) REVERT: K 73 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8421 (mm110) REVERT: L 256 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.7193 (m-80) REVERT: L 274 ARG cc_start: 0.9332 (ttm110) cc_final: 0.9100 (mmp80) REVERT: L 277 MET cc_start: 0.8554 (tpp) cc_final: 0.7593 (tpp) REVERT: L 486 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8316 (mmm160) REVERT: L 515 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7855 (tp30) outliers start: 56 outliers final: 26 residues processed: 313 average time/residue: 0.8207 time to fit residues: 297.2564 Evaluate side-chains 272 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1038 GLN Chi-restraints excluded: chain I residue 1127 LYS Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 1188 GLU Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain L residue 256 PHE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 271 ASN Chi-restraints excluded: chain L residue 486 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 27 optimal weight: 9.9990 chunk 375 optimal weight: 10.0000 chunk 323 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 302 optimal weight: 5.9990 chunk 312 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 177 optimal weight: 0.8980 chunk 227 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 667 GLN ** H 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.099476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.057961 restraints weight = 61706.292| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.51 r_work: 0.2539 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2396 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32196 Z= 0.183 Angle : 0.535 8.651 43973 Z= 0.291 Chirality : 0.042 0.267 5011 Planarity : 0.004 0.059 5327 Dihedral : 16.444 174.130 5414 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.90 % Allowed : 12.48 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % 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: 0.92 (0.14), residues: 3676 helix: 1.82 (0.14), residues: 1474 sheet: 0.75 (0.24), residues: 480 loop : -0.48 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I1034 TYR 0.015 0.001 TYR J 631 PHE 0.012 0.001 PHE I 972 TRP 0.009 0.001 TRP I 997 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (32188) covalent geometry : angle 0.53323 / 0.29 (43961) hydrogen bonds : bond 0.04698 / 3.11 ( 1453) hydrogen bonds : angle 4.24190 / 2.96 ( 4002) metal coordination : bond 0.00694 / 0.35 ( 8) metal coordination : angle 2.77827 / 1.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 244 time to evaluate : 1.400 Fit side-chains REVERT: I 126 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8613 (mm-30) REVERT: I 131 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8717 (p) REVERT: I 240 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8547 (tp30) REVERT: I 272 ARG cc_start: 0.9048 (mmm160) cc_final: 0.8487 (mmp80) REVERT: I 315 MET cc_start: 0.8940 (ttp) cc_final: 0.8271 (mtm) REVERT: I 325 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.8988 (mp) REVERT: I 369 MET cc_start: 0.8914 (tmm) cc_final: 0.8650 (tmm) REVERT: I 492 MET cc_start: 0.9325 (mtm) cc_final: 0.9107 (mtm) REVERT: I 899 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7841 (tm-30) REVERT: I 997 TRP cc_start: 0.7969 (m-10) cc_final: 0.7744 (m-10) REVERT: I 1025 PHE cc_start: 0.7947 (t80) cc_final: 0.7731 (t80) REVERT: I 1127 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8515 (mptm) REVERT: J 60 ARG cc_start: 0.8827 (ttp80) cc_final: 0.8202 (ttp80) REVERT: J 177 ASP cc_start: 0.8738 (t0) cc_final: 0.7881 (p0) REVERT: J 827 GLU cc_start: 0.8759 (pt0) cc_final: 0.8295 (pp20) REVERT: J 844 THR cc_start: 0.9377 (OUTLIER) cc_final: 0.9161 (p) REVERT: J 873 GLU cc_start: 0.9121 (tp30) cc_final: 0.8725 (tp30) REVERT: J 1063 ASP cc_start: 0.8692 (t0) cc_final: 0.8469 (t0) REVERT: J 1084 GLN cc_start: 0.8736 (pm20) cc_final: 0.8274 (pp30) REVERT: J 1086 ASN cc_start: 0.9215 (t0) cc_final: 0.8766 (m110) REVERT: J 1108 GLN cc_start: 0.9433 (tt0) cc_final: 0.9100 (mm-40) REVERT: J 1143 ASP cc_start: 0.8732 (m-30) cc_final: 0.8491 (m-30) REVERT: J 1188 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8534 (tm-30) REVERT: J 1189 MET cc_start: 0.8996 (mmp) cc_final: 0.8658 (mmm) REVERT: J 1195 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7424 (tm-30) REVERT: J 1334 GLU cc_start: 0.8923 (tp30) cc_final: 0.8664 (tp30) REVERT: K 41 GLU cc_start: 0.9028 (pt0) cc_final: 0.8446 (pp20) REVERT: K 68 GLU cc_start: 0.8231 (tm-30) cc_final: 0.8025 (tm-30) REVERT: H 127 GLN cc_start: 0.9133 (mp10) cc_final: 0.8816 (pm20) REVERT: L 256 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6936 (m-80) REVERT: L 274 ARG cc_start: 0.9389 (ttm110) cc_final: 0.9129 (mmp80) REVERT: L 277 MET cc_start: 0.8698 (tpp) cc_final: 0.7650 (tpp) REVERT: L 362 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.7892 (t0) REVERT: L 365 MET cc_start: 0.8626 (ppp) cc_final: 0.8371 (ppp) REVERT: L 486 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8408 (mmm160) outliers start: 60 outliers final: 32 residues processed: 291 average time/residue: 0.7643 time to fit residues: 257.8025 Evaluate side-chains 274 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 233 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1127 LYS Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 1188 GLU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain L residue 256 PHE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 271 ASN Chi-restraints excluded: chain L residue 362 ASN Chi-restraints excluded: chain L residue 486 ARG Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 598 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 313 optimal weight: 0.0000 chunk 236 optimal weight: 10.0000 chunk 291 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 365 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 328 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 361 optimal weight: 3.9990 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 147 GLN H 66 HIS H 147 GLN ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.098913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.057552 restraints weight = 61580.969| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.50 r_work: 0.2533 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2391 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32196 Z= 0.182 Angle : 0.532 8.033 43973 Z= 0.288 Chirality : 0.042 0.272 5011 Planarity : 0.004 0.064 5327 Dihedral : 16.461 173.419 5414 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.87 % Allowed : 13.17 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.14), residues: 3676 helix: 1.94 (0.14), residues: 1468 sheet: 0.78 (0.24), residues: 480 loop : -0.45 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 275 TYR 0.014 0.001 TYR J 631 PHE 0.017 0.001 PHE I 545 TRP 0.010 0.001 TRP L 326 HIS 0.003 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (32188) covalent geometry : angle 0.53030 / 0.29 (43961) hydrogen bonds : bond 0.04503 / 2.98 ( 1453) hydrogen bonds : angle 4.14509 / 2.89 ( 4002) metal coordination : bond 0.00638 / 0.33 ( 8) metal coordination : angle 2.80335 / 1.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 245 time to evaluate : 1.306 Fit side-chains revert: symmetry clash REVERT: I 81 ASP cc_start: 0.8294 (t0) cc_final: 0.8077 (t0) REVERT: I 240 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8559 (tp30) REVERT: I 268 ARG cc_start: 0.8749 (ttp80) cc_final: 0.8507 (ppt170) REVERT: I 272 ARG cc_start: 0.9107 (mmm160) cc_final: 0.8599 (mmp80) REVERT: I 277 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8975 (mm) REVERT: I 283 LYS cc_start: 0.8566 (mmmt) cc_final: 0.8276 (mmmt) REVERT: I 315 MET cc_start: 0.8936 (ttp) cc_final: 0.8262 (mtm) REVERT: I 325 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9052 (mp) REVERT: I 369 MET cc_start: 0.8942 (tmm) cc_final: 0.8703 (tmm) REVERT: I 394 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8243 (mtm180) REVERT: I 492 MET cc_start: 0.9318 (mtm) cc_final: 0.9087 (mtm) REVERT: I 542 ARG cc_start: 0.7926 (mtp85) cc_final: 0.7396 (mtm110) REVERT: I 899 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7846 (tm-30) REVERT: I 965 GLN cc_start: 0.8810 (tp-100) cc_final: 0.8558 (tp-100) REVERT: I 1127 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8517 (mptm) REVERT: J 177 ASP cc_start: 0.8771 (t0) cc_final: 0.7922 (p0) REVERT: J 200 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8416 (mp10) REVERT: J 388 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7547 (mtt180) REVERT: J 798 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8438 (ttt180) REVERT: J 827 GLU cc_start: 0.8762 (pt0) cc_final: 0.8327 (pp20) REVERT: J 844 THR cc_start: 0.9383 (OUTLIER) cc_final: 0.9162 (p) REVERT: J 873 GLU cc_start: 0.9126 (tp30) cc_final: 0.8727 (tp30) REVERT: J 947 GLU cc_start: 0.8213 (tp30) cc_final: 0.8010 (tp30) REVERT: J 1084 GLN cc_start: 0.8733 (pm20) cc_final: 0.8318 (pp30) REVERT: J 1086 ASN cc_start: 0.9217 (t0) cc_final: 0.8757 (m110) REVERT: J 1108 GLN cc_start: 0.9439 (tt0) cc_final: 0.9064 (mm-40) REVERT: J 1143 ASP cc_start: 0.8804 (m-30) cc_final: 0.8524 (m-30) REVERT: J 1188 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8492 (tm-30) REVERT: J 1189 MET cc_start: 0.8998 (mmp) cc_final: 0.8594 (mmm) REVERT: J 1195 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7310 (tm-30) REVERT: J 1334 GLU cc_start: 0.8944 (tp30) cc_final: 0.8705 (tp30) REVERT: K 41 GLU cc_start: 0.9022 (pt0) cc_final: 0.8461 (pp20) REVERT: K 71 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: K 73 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8284 (mm-40) REVERT: H 127 GLN cc_start: 0.9110 (mp10) cc_final: 0.8856 (pm20) REVERT: L 256 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.7037 (m-80) REVERT: L 273 MET cc_start: 0.8536 (tpt) cc_final: 0.7680 (tpp) REVERT: L 274 ARG cc_start: 0.9408 (ttm110) cc_final: 0.9065 (tpp-160) REVERT: L 277 MET cc_start: 0.8681 (tpp) cc_final: 0.8068 (tpp) REVERT: L 486 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8493 (mmm160) REVERT: L 508 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8631 (mp0) outliers start: 59 outliers final: 33 residues processed: 291 average time/residue: 0.8327 time to fit residues: 280.8853 Evaluate side-chains 280 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 235 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1127 LYS Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 388 ARG Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 798 ARG Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 1188 GLU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 256 PHE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 271 ASN Chi-restraints excluded: chain L residue 486 ARG Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 598 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 265 optimal weight: 2.9990 chunk 288 optimal weight: 1.9990 chunk 303 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 325 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 350 optimal weight: 7.9990 chunk 370 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 66 HIS H 147 GLN ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.098813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.057473 restraints weight = 61576.066| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 2.50 r_work: 0.2537 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2396 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32196 Z= 0.171 Angle : 0.526 7.773 43973 Z= 0.285 Chirality : 0.042 0.276 5011 Planarity : 0.004 0.067 5327 Dihedral : 16.462 173.085 5413 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.06 % Allowed : 13.24 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.14), residues: 3676 helix: 2.02 (0.14), residues: 1468 sheet: 0.79 (0.24), residues: 482 loop : -0.44 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I1034 TYR 0.014 0.001 TYR J 631 PHE 0.011 0.001 PHE J1319 TRP 0.011 0.001 TRP I 997 HIS 0.003 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (32188) covalent geometry : angle 0.52434 / 0.28 (43961) hydrogen bonds : bond 0.04364 / 2.88 ( 1453) hydrogen bonds : angle 4.08886 / 2.85 ( 4002) metal coordination : bond 0.00596 / 0.31 ( 8) metal coordination : angle 2.66641 / 1.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 244 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: I 81 ASP cc_start: 0.8282 (t0) cc_final: 0.8071 (t0) REVERT: I 240 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8572 (tp30) REVERT: I 268 ARG cc_start: 0.8736 (ttp80) cc_final: 0.8446 (ppt170) REVERT: I 277 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8964 (mm) REVERT: I 283 LYS cc_start: 0.8608 (mmmt) cc_final: 0.8398 (mmmt) REVERT: I 315 MET cc_start: 0.8947 (ttp) cc_final: 0.8270 (mtm) REVERT: I 325 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9057 (mp) REVERT: I 369 MET cc_start: 0.8960 (tmm) cc_final: 0.8719 (tmm) REVERT: I 394 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8223 (mtm180) REVERT: I 542 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7411 (mtm110) REVERT: I 899 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7885 (tm-30) REVERT: I 965 GLN cc_start: 0.8850 (tp-100) cc_final: 0.8539 (tp-100) REVERT: I 997 TRP cc_start: 0.8012 (m-10) cc_final: 0.7755 (m-10) REVERT: I 1025 PHE cc_start: 0.7978 (t80) cc_final: 0.7748 (t80) REVERT: I 1027 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.9017 (mmtt) REVERT: I 1127 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8514 (mptm) REVERT: J 177 ASP cc_start: 0.8768 (t0) cc_final: 0.7930 (p0) REVERT: J 200 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8413 (mp10) REVERT: J 798 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8424 (ttt180) REVERT: J 827 GLU cc_start: 0.8733 (pt0) cc_final: 0.8389 (pp20) REVERT: J 844 THR cc_start: 0.9391 (OUTLIER) cc_final: 0.9162 (p) REVERT: J 873 GLU cc_start: 0.9129 (tp30) cc_final: 0.8731 (tp30) REVERT: J 1063 ASP cc_start: 0.8467 (t0) cc_final: 0.8197 (t0) REVERT: J 1084 GLN cc_start: 0.8752 (pm20) cc_final: 0.8403 (pp30) REVERT: J 1086 ASN cc_start: 0.9225 (t0) cc_final: 0.8762 (m110) REVERT: J 1108 GLN cc_start: 0.9438 (tt0) cc_final: 0.9071 (mm-40) REVERT: J 1188 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8478 (tm-30) REVERT: J 1189 MET cc_start: 0.8977 (mmp) cc_final: 0.8537 (mmm) REVERT: J 1195 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7361 (tm-30) REVERT: J 1334 GLU cc_start: 0.8937 (tp30) cc_final: 0.8714 (tp30) REVERT: K 41 GLU cc_start: 0.9030 (pt0) cc_final: 0.8484 (pp20) REVERT: H 127 GLN cc_start: 0.9119 (mp10) cc_final: 0.8865 (pm20) REVERT: L 137 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.7320 (t80) REVERT: L 256 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.7060 (m-80) REVERT: L 273 MET cc_start: 0.8575 (tpt) cc_final: 0.7823 (tpp) REVERT: L 274 ARG cc_start: 0.9408 (ttm110) cc_final: 0.9104 (mmm160) REVERT: L 277 MET cc_start: 0.8723 (tpp) cc_final: 0.8031 (tpp) REVERT: L 297 MET cc_start: 0.0591 (ptm) cc_final: 0.0380 (ptm) REVERT: L 322 MET cc_start: 0.7425 (pp-130) cc_final: 0.7058 (pp-130) REVERT: L 486 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8500 (mmm160) outliers start: 65 outliers final: 39 residues processed: 298 average time/residue: 0.7514 time to fit residues: 261.0061 Evaluate side-chains 287 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 236 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1027 LYS Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1127 LYS Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 798 ARG Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1188 GLU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 256 PHE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 271 ASN Chi-restraints excluded: chain L residue 486 ARG Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 598 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 196 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 297 optimal weight: 2.9990 chunk 327 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 113 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 66 HIS ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 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 = 0.098230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.056777 restraints weight = 61405.026| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 2.50 r_work: 0.2522 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2381 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9110 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 32196 Z= 0.205 Angle : 0.544 8.150 43973 Z= 0.293 Chirality : 0.043 0.277 5011 Planarity : 0.004 0.072 5327 Dihedral : 16.507 172.982 5413 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.25 % Allowed : 13.71 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.14), residues: 3676 helix: 2.01 (0.14), residues: 1468 sheet: 0.78 (0.24), residues: 482 loop : -0.46 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG I1034 TYR 0.014 0.001 TYR J 631 PHE 0.016 0.001 PHE I 545 TRP 0.009 0.001 TRP L 326 HIS 0.004 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.20 (32188) covalent geometry : angle 0.54198 / 0.29 (43961) hydrogen bonds : bond 0.04622 / 3.06 ( 1453) hydrogen bonds : angle 4.09769 / 2.85 ( 4002) metal coordination : bond 0.00744 / 0.38 ( 8) metal coordination : angle 2.85522 / 1.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 242 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 81 ASP cc_start: 0.8286 (t0) cc_final: 0.8074 (t0) REVERT: I 126 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8560 (mm-30) REVERT: I 268 ARG cc_start: 0.8721 (ttp80) cc_final: 0.8428 (ppt170) REVERT: I 272 ARG cc_start: 0.9330 (tpp-160) cc_final: 0.8889 (mmp80) REVERT: I 277 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8933 (mm) REVERT: I 291 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.8192 (t80) REVERT: I 315 MET cc_start: 0.8950 (ttp) cc_final: 0.8266 (mtm) REVERT: I 325 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9105 (mp) REVERT: I 394 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8216 (mtm180) REVERT: I 542 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7358 (mtm110) REVERT: I 899 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7906 (tm-30) REVERT: I 965 GLN cc_start: 0.8882 (tp-100) cc_final: 0.8548 (tp-100) REVERT: I 1025 PHE cc_start: 0.7979 (t80) cc_final: 0.7745 (t80) REVERT: I 1127 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8529 (mptm) REVERT: J 177 ASP cc_start: 0.8774 (t0) cc_final: 0.7948 (p0) REVERT: J 200 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8382 (mp10) REVERT: J 798 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8441 (ttt180) REVERT: J 827 GLU cc_start: 0.8703 (pt0) cc_final: 0.8368 (pp20) REVERT: J 844 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.9145 (p) REVERT: J 873 GLU cc_start: 0.9135 (tp30) cc_final: 0.8738 (tp30) REVERT: J 1063 ASP cc_start: 0.8523 (t0) cc_final: 0.8136 (t0) REVERT: J 1084 GLN cc_start: 0.8761 (pm20) cc_final: 0.8408 (pp30) REVERT: J 1086 ASN cc_start: 0.9212 (t0) cc_final: 0.8767 (m110) REVERT: J 1108 GLN cc_start: 0.9458 (OUTLIER) cc_final: 0.9068 (mm-40) REVERT: J 1188 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8487 (tm-30) REVERT: J 1189 MET cc_start: 0.9012 (mmp) cc_final: 0.8561 (mmp) REVERT: J 1195 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7440 (tm-30) REVERT: J 1334 GLU cc_start: 0.8939 (tp30) cc_final: 0.8730 (tp30) REVERT: K 41 GLU cc_start: 0.9051 (pt0) cc_final: 0.8519 (pp20) REVERT: H 127 GLN cc_start: 0.9124 (mp10) cc_final: 0.8873 (pm20) REVERT: L 137 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7322 (t80) REVERT: L 256 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.7127 (m-80) REVERT: L 273 MET cc_start: 0.8631 (tpt) cc_final: 0.7856 (tpp) REVERT: L 274 ARG cc_start: 0.9414 (ttm110) cc_final: 0.9102 (mmm160) REVERT: L 277 MET cc_start: 0.8828 (tpp) cc_final: 0.7826 (tpt) REVERT: L 322 MET cc_start: 0.7479 (pp-130) cc_final: 0.7082 (pp-130) REVERT: L 486 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8508 (mmm160) outliers start: 71 outliers final: 44 residues processed: 300 average time/residue: 0.7581 time to fit residues: 264.0421 Evaluate side-chains 293 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 235 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1127 LYS Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 798 ARG Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1108 GLN Chi-restraints excluded: chain J residue 1188 GLU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 256 PHE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 271 ASN Chi-restraints excluded: chain L residue 365 MET Chi-restraints excluded: chain L residue 486 ARG Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 598 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 240 optimal weight: 7.9990 chunk 260 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 268 optimal weight: 5.9990 chunk 302 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 257 optimal weight: 0.7980 chunk 177 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 554 HIS H 66 HIS H 93 GLN ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.099687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.058402 restraints weight = 61597.098| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.52 r_work: 0.2560 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32196 Z= 0.111 Angle : 0.514 15.643 43973 Z= 0.276 Chirality : 0.041 0.283 5011 Planarity : 0.004 0.078 5327 Dihedral : 16.405 172.746 5413 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.96 % Allowed : 14.25 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.14), residues: 3676 helix: 2.13 (0.14), residues: 1473 sheet: 0.93 (0.24), residues: 480 loop : -0.37 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG I1034 TYR 0.013 0.001 TYR J 631 PHE 0.011 0.001 PHE J1319 TRP 0.016 0.001 TRP I 997 HIS 0.003 0.000 HIS J 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (32188) covalent geometry : angle 0.51245 / 0.28 (43961) hydrogen bonds : bond 0.03694 / 2.44 ( 1453) hydrogen bonds : angle 3.96317 / 2.76 ( 4002) metal coordination : bond 0.00355 / 0.21 ( 8) metal coordination : angle 2.24034 / 1.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 248 time to evaluate : 1.245 Fit side-chains REVERT: I 5 TYR cc_start: 0.8108 (m-80) cc_final: 0.7860 (m-80) REVERT: I 81 ASP cc_start: 0.8266 (t0) cc_final: 0.8057 (t0) REVERT: I 268 ARG cc_start: 0.8720 (ttp80) cc_final: 0.8417 (ppt170) REVERT: I 272 ARG cc_start: 0.9306 (tpp-160) cc_final: 0.8479 (mmp80) REVERT: I 277 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8943 (mm) REVERT: I 291 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.8251 (t80) REVERT: I 315 MET cc_start: 0.8970 (ttp) cc_final: 0.8372 (mtm) REVERT: I 325 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9118 (mp) REVERT: I 394 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8352 (mmm160) REVERT: I 465 ARG cc_start: 0.8608 (ttm110) cc_final: 0.8188 (ttp-110) REVERT: I 542 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7314 (mtm110) REVERT: I 899 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7848 (tm-30) REVERT: I 965 GLN cc_start: 0.8884 (tp-100) cc_final: 0.8543 (tp-100) REVERT: I 997 TRP cc_start: 0.7947 (m-10) cc_final: 0.7708 (m-10) REVERT: I 1025 PHE cc_start: 0.7953 (t80) cc_final: 0.7724 (t80) REVERT: I 1041 ASP cc_start: 0.9019 (t0) cc_final: 0.8542 (p0) REVERT: I 1127 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8553 (mptm) REVERT: I 1219 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8872 (mt-10) REVERT: J 177 ASP cc_start: 0.8769 (t0) cc_final: 0.7950 (p0) REVERT: J 200 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8395 (mp10) REVERT: J 227 PHE cc_start: 0.9207 (OUTLIER) cc_final: 0.8183 (t80) REVERT: J 827 GLU cc_start: 0.8696 (pt0) cc_final: 0.8367 (pp20) REVERT: J 849 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8718 (mt) REVERT: J 873 GLU cc_start: 0.9127 (tp30) cc_final: 0.8733 (tp30) REVERT: J 1063 ASP cc_start: 0.8556 (t0) cc_final: 0.8166 (t0) REVERT: J 1086 ASN cc_start: 0.9224 (t0) cc_final: 0.8876 (m-40) REVERT: J 1108 GLN cc_start: 0.9446 (OUTLIER) cc_final: 0.9080 (mm-40) REVERT: J 1195 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7357 (tm-30) REVERT: J 1334 GLU cc_start: 0.8920 (tp30) cc_final: 0.8686 (tp30) REVERT: K 41 GLU cc_start: 0.9046 (pt0) cc_final: 0.8573 (pp20) REVERT: G 33 ARG cc_start: 0.8685 (ttm-80) cc_final: 0.8390 (ttm-80) REVERT: H 127 GLN cc_start: 0.9113 (mp10) cc_final: 0.8853 (pm20) REVERT: L 137 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.7286 (t80) REVERT: L 256 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.7128 (m-80) REVERT: L 273 MET cc_start: 0.8593 (tpt) cc_final: 0.8341 (tpp) REVERT: L 274 ARG cc_start: 0.9405 (ttm110) cc_final: 0.9057 (mmm160) REVERT: L 277 MET cc_start: 0.8831 (tpp) cc_final: 0.7656 (tpt) REVERT: L 278 ASP cc_start: 0.9253 (m-30) cc_final: 0.8932 (m-30) REVERT: L 365 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8495 (ppp) REVERT: L 477 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8414 (tp30) REVERT: L 486 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8509 (mmm160) outliers start: 62 outliers final: 34 residues processed: 299 average time/residue: 0.8082 time to fit residues: 281.1430 Evaluate side-chains 286 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1127 LYS Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1108 GLN Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 105 MET Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 256 PHE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 271 ASN Chi-restraints excluded: chain L residue 365 MET Chi-restraints excluded: chain L residue 486 ARG Chi-restraints excluded: chain L residue 552 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 7 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 318 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 262 optimal weight: 7.9990 chunk 233 optimal weight: 10.0000 chunk 26 optimal weight: 0.0970 chunk 323 optimal weight: 5.9990 chunk 329 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 199 optimal weight: 7.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 667 GLN J 861 ASN H 66 HIS ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.097416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.055855 restraints weight = 62053.522| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 2.51 r_work: 0.2501 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2360 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 32196 Z= 0.285 Angle : 0.622 23.056 43973 Z= 0.329 Chirality : 0.045 0.278 5011 Planarity : 0.007 0.373 5327 Dihedral : 16.564 173.407 5413 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.06 % Allowed : 14.53 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.14), residues: 3676 helix: 1.92 (0.14), residues: 1482 sheet: 0.78 (0.25), residues: 466 loop : -0.47 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.001 ARG I 272 TYR 0.016 0.001 TYR J 631 PHE 0.013 0.001 PHE I 545 TRP 0.009 0.001 TRP J 580 HIS 0.011 0.001 HIS I 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.28 (32188) covalent geometry : angle 0.61975 / 0.33 (43961) hydrogen bonds : bond 0.05119 / 3.39 ( 1453) hydrogen bonds : angle 4.15663 / 2.89 ( 4002) metal coordination : bond 0.01028 / 0.50 ( 8) metal coordination : angle 3.19493 / 1.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 239 time to evaluate : 1.163 Fit side-chains REVERT: I 81 ASP cc_start: 0.8304 (t0) cc_final: 0.8083 (t0) REVERT: I 268 ARG cc_start: 0.8755 (ttp80) cc_final: 0.8473 (ppt170) REVERT: I 277 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8999 (mm) REVERT: I 291 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.8214 (t80) REVERT: I 315 MET cc_start: 0.8966 (ttp) cc_final: 0.8295 (mtm) REVERT: I 325 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9134 (mp) REVERT: I 394 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8262 (mtm180) REVERT: I 542 ARG cc_start: 0.7902 (mtp85) cc_final: 0.7360 (mtm110) REVERT: I 899 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7910 (tm-30) REVERT: I 965 GLN cc_start: 0.8894 (tp-100) cc_final: 0.8556 (tp-100) REVERT: I 1025 PHE cc_start: 0.7997 (t80) cc_final: 0.7787 (t80) REVERT: I 1027 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.9032 (mmtt) REVERT: I 1041 ASP cc_start: 0.9038 (t0) cc_final: 0.8530 (p0) REVERT: I 1127 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8568 (mptm) REVERT: J 177 ASP cc_start: 0.8791 (t0) cc_final: 0.7922 (p0) REVERT: J 200 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8390 (mp10) REVERT: J 227 PHE cc_start: 0.9246 (OUTLIER) cc_final: 0.8198 (t80) REVERT: J 827 GLU cc_start: 0.8691 (pt0) cc_final: 0.8358 (pp20) REVERT: J 873 GLU cc_start: 0.9128 (tp30) cc_final: 0.8728 (tp30) REVERT: J 1040 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7551 (mtm) REVERT: J 1063 ASP cc_start: 0.8578 (t0) cc_final: 0.8149 (t70) REVERT: J 1086 ASN cc_start: 0.9217 (t0) cc_final: 0.8881 (m110) REVERT: J 1108 GLN cc_start: 0.9468 (OUTLIER) cc_final: 0.9077 (mm-40) REVERT: J 1189 MET cc_start: 0.9056 (mmm) cc_final: 0.8835 (mmm) REVERT: J 1195 GLN cc_start: 0.8068 (tm-30) cc_final: 0.7446 (tm-30) REVERT: J 1334 GLU cc_start: 0.8964 (tp30) cc_final: 0.8758 (tp30) REVERT: K 41 GLU cc_start: 0.9038 (pt0) cc_final: 0.8563 (pp20) REVERT: H 127 GLN cc_start: 0.9133 (mp10) cc_final: 0.8866 (pm20) REVERT: L 137 TYR cc_start: 0.7793 (OUTLIER) cc_final: 0.7363 (t80) REVERT: L 256 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.7110 (m-80) REVERT: L 273 MET cc_start: 0.8615 (tpt) cc_final: 0.7862 (tpp) REVERT: L 274 ARG cc_start: 0.9426 (ttm110) cc_final: 0.9106 (mmm160) REVERT: L 277 MET cc_start: 0.8871 (tpp) cc_final: 0.7765 (tpt) REVERT: L 322 MET cc_start: 0.7468 (pp-130) cc_final: 0.7250 (pp-130) REVERT: L 477 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8361 (tp30) REVERT: L 486 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8543 (mmm160) outliers start: 65 outliers final: 40 residues processed: 291 average time/residue: 0.7835 time to fit residues: 265.8770 Evaluate side-chains 286 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 233 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 1027 LYS Chi-restraints excluded: chain I residue 1038 GLN Chi-restraints excluded: chain I residue 1127 LYS Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1219 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1108 GLN Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 256 PHE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 271 ASN Chi-restraints excluded: chain L residue 365 MET Chi-restraints excluded: chain L residue 486 ARG Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 598 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 140 optimal weight: 0.5980 chunk 185 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 233 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN H 66 HIS H 147 GLN ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.099219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.058052 restraints weight = 61167.661| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.50 r_work: 0.2552 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9090 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32196 Z= 0.128 Angle : 0.539 13.724 43973 Z= 0.288 Chirality : 0.041 0.285 5011 Planarity : 0.004 0.084 5327 Dihedral : 16.442 172.876 5413 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.71 % Allowed : 14.98 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.14), residues: 3676 helix: 2.07 (0.14), residues: 1475 sheet: 0.96 (0.24), residues: 479 loop : -0.38 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG I1034 TYR 0.013 0.001 TYR J 631 PHE 0.011 0.001 PHE J1319 TRP 0.022 0.001 TRP I 997 HIS 0.005 0.001 HIS L 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (32188) covalent geometry : angle 0.53773 / 0.29 (43961) hydrogen bonds : bond 0.03813 / 2.52 ( 1453) hydrogen bonds : angle 3.98758 / 2.77 ( 4002) metal coordination : bond 0.00357 / 0.19 ( 8) metal coordination : angle 2.29542 / 1.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 242 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: I 81 ASP cc_start: 0.8299 (t0) cc_final: 0.8088 (t0) REVERT: I 268 ARG cc_start: 0.8737 (ttp80) cc_final: 0.8428 (ppt170) REVERT: I 277 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8820 (mm) REVERT: I 291 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.8168 (t80) REVERT: I 315 MET cc_start: 0.8981 (ttp) cc_final: 0.8374 (mtm) REVERT: I 325 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9148 (mp) REVERT: I 394 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8274 (mmm160) REVERT: I 542 ARG cc_start: 0.7910 (mtp85) cc_final: 0.7321 (mtm110) REVERT: I 899 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7831 (tm-30) REVERT: I 965 GLN cc_start: 0.8880 (tp-100) cc_final: 0.8552 (tp-100) REVERT: I 1025 PHE cc_start: 0.7953 (t80) cc_final: 0.7713 (t80) REVERT: I 1041 ASP cc_start: 0.9042 (t0) cc_final: 0.8538 (p0) REVERT: I 1127 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8595 (mptm) REVERT: J 66 LYS cc_start: 0.8713 (mttp) cc_final: 0.8383 (mtpp) REVERT: J 177 ASP cc_start: 0.8763 (t0) cc_final: 0.7911 (p0) REVERT: J 200 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8364 (mp10) REVERT: J 227 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8242 (t80) REVERT: J 827 GLU cc_start: 0.8691 (pt0) cc_final: 0.8409 (pp20) REVERT: J 873 GLU cc_start: 0.9136 (tp30) cc_final: 0.8754 (tp30) REVERT: J 1040 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7441 (mtm) REVERT: J 1063 ASP cc_start: 0.8604 (t0) cc_final: 0.8169 (t70) REVERT: J 1086 ASN cc_start: 0.9214 (t0) cc_final: 0.8884 (m110) REVERT: J 1108 GLN cc_start: 0.9448 (OUTLIER) cc_final: 0.9080 (mm-40) REVERT: J 1195 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7340 (tm-30) REVERT: J 1334 GLU cc_start: 0.8924 (tp30) cc_final: 0.8704 (tp30) REVERT: K 41 GLU cc_start: 0.9036 (pt0) cc_final: 0.8576 (pp20) REVERT: G 33 ARG cc_start: 0.8684 (ttm-80) cc_final: 0.8411 (ttm-80) REVERT: L 137 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.7462 (t80) REVERT: L 256 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.7117 (m-80) REVERT: L 273 MET cc_start: 0.8596 (tpt) cc_final: 0.8206 (tpp) REVERT: L 274 ARG cc_start: 0.9423 (ttm110) cc_final: 0.9125 (mmm160) REVERT: L 277 MET cc_start: 0.8883 (tpp) cc_final: 0.7859 (tpt) REVERT: L 322 MET cc_start: 0.7402 (pp-130) cc_final: 0.7174 (pp-130) REVERT: L 365 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8417 (ppp) REVERT: L 486 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8552 (mmm160) outliers start: 54 outliers final: 31 residues processed: 284 average time/residue: 0.8906 time to fit residues: 293.7401 Evaluate side-chains 279 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 235 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 1127 LYS Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1108 GLN Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 256 PHE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 271 ASN Chi-restraints excluded: chain L residue 365 MET Chi-restraints excluded: chain L residue 486 ARG Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 598 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 339 optimal weight: 5.9990 chunk 305 optimal weight: 0.4980 chunk 176 optimal weight: 0.0980 chunk 237 optimal weight: 10.0000 chunk 279 optimal weight: 20.0000 chunk 164 optimal weight: 0.0010 chunk 238 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 357 optimal weight: 0.9980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN H 66 HIS H 93 GLN H 147 GLN ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.100183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.059084 restraints weight = 61583.280| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.52 r_work: 0.2576 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 32196 Z= 0.106 Angle : 0.537 13.757 43973 Z= 0.286 Chirality : 0.041 0.283 5011 Planarity : 0.004 0.065 5327 Dihedral : 16.328 173.393 5413 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.55 % Allowed : 15.33 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.14), residues: 3676 helix: 2.16 (0.14), residues: 1477 sheet: 1.00 (0.24), residues: 486 loop : -0.30 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG L 339 TYR 0.012 0.001 TYR J 631 PHE 0.014 0.001 PHE I 545 TRP 0.029 0.001 TRP I 997 HIS 0.007 0.000 HIS L 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (32188) covalent geometry : angle 0.53619 / 0.29 (43961) hydrogen bonds : bond 0.03421 / 2.24 ( 1453) hydrogen bonds : angle 3.89915 / 2.71 ( 4002) metal coordination : bond 0.00261 / 0.15 ( 8) metal coordination : angle 2.18094 / 1.26 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7352 Ramachandran restraints generated. 3676 Oldfield, 0 Emsley, 3676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 245 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 81 ASP cc_start: 0.8306 (t0) cc_final: 0.8105 (t0) REVERT: I 268 ARG cc_start: 0.8758 (ttp80) cc_final: 0.8469 (ppt170) REVERT: I 277 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8874 (mm) REVERT: I 291 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.8152 (t80) REVERT: I 315 MET cc_start: 0.8970 (ttp) cc_final: 0.8371 (mtm) REVERT: I 325 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9266 (mp) REVERT: I 394 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8258 (mmm160) REVERT: I 542 ARG cc_start: 0.7891 (mtp85) cc_final: 0.7319 (mtm110) REVERT: I 899 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7800 (tm-30) REVERT: I 965 GLN cc_start: 0.8879 (tp-100) cc_final: 0.8554 (tp-100) REVERT: I 1025 PHE cc_start: 0.7920 (t80) cc_final: 0.7668 (t80) REVERT: I 1041 ASP cc_start: 0.9025 (t0) cc_final: 0.8518 (p0) REVERT: I 1127 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8513 (mptm) REVERT: I 1289 GLU cc_start: 0.8779 (tt0) cc_final: 0.8354 (tt0) REVERT: J 66 LYS cc_start: 0.8684 (mttp) cc_final: 0.8363 (mtpp) REVERT: J 177 ASP cc_start: 0.8764 (t0) cc_final: 0.7902 (p0) REVERT: J 200 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8362 (mp10) REVERT: J 227 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8264 (t80) REVERT: J 329 ASP cc_start: 0.9167 (m-30) cc_final: 0.8925 (m-30) REVERT: J 827 GLU cc_start: 0.8692 (pt0) cc_final: 0.8408 (pp20) REVERT: J 849 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8768 (mt) REVERT: J 873 GLU cc_start: 0.9135 (tp30) cc_final: 0.8750 (tp30) REVERT: J 1040 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7336 (mtm) REVERT: J 1063 ASP cc_start: 0.8621 (t0) cc_final: 0.8195 (t70) REVERT: J 1086 ASN cc_start: 0.9211 (t0) cc_final: 0.8900 (m110) REVERT: J 1108 GLN cc_start: 0.9451 (OUTLIER) cc_final: 0.9066 (mm-40) REVERT: J 1195 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7334 (tm-30) REVERT: J 1334 GLU cc_start: 0.8915 (tp30) cc_final: 0.8684 (tp30) REVERT: K 41 GLU cc_start: 0.9025 (pt0) cc_final: 0.8579 (pp20) REVERT: G 33 ARG cc_start: 0.8671 (ttm-80) cc_final: 0.8390 (ttm-80) REVERT: L 98 VAL cc_start: 0.9199 (OUTLIER) cc_final: 0.8990 (p) REVERT: L 137 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.7317 (t80) REVERT: L 256 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.7007 (m-80) REVERT: L 277 MET cc_start: 0.8812 (tpp) cc_final: 0.8407 (tpt) REVERT: L 322 MET cc_start: 0.7436 (pp-130) cc_final: 0.7232 (pp-130) REVERT: L 365 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8518 (ppp) REVERT: L 477 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8422 (tp30) REVERT: L 486 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8558 (mmm160) outliers start: 49 outliers final: 27 residues processed: 281 average time/residue: 0.7711 time to fit residues: 251.7065 Evaluate side-chains 279 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 237 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 291 TYR Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 394 ARG Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 484 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 685 MET Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 1127 LYS Chi-restraints excluded: chain I residue 1184 THR Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain J residue 1108 GLN Chi-restraints excluded: chain J residue 1243 LEU Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 163 THR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 256 PHE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 271 ASN Chi-restraints excluded: chain L residue 365 MET Chi-restraints excluded: chain L residue 486 ARG Chi-restraints excluded: chain L residue 552 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 196 optimal weight: 7.9990 chunk 62 optimal weight: 0.0870 chunk 104 optimal weight: 5.9990 chunk 333 optimal weight: 20.0000 chunk 234 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 370 optimal weight: 2.9990 chunk 347 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 273 HIS H 66 HIS H 147 GLN ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 568 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.100074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.058900 restraints weight = 61362.565| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.52 r_work: 0.2575 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2435 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32196 Z= 0.115 Angle : 0.547 13.978 43973 Z= 0.289 Chirality : 0.041 0.284 5011 Planarity : 0.004 0.059 5327 Dihedral : 16.320 173.488 5412 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.46 % Allowed : 15.48 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.14), residues: 3676 helix: 2.20 (0.14), residues: 1475 sheet: 1.03 (0.25), residues: 480 loop : -0.28 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 275 TYR 0.024 0.001 TYR L 137 PHE 0.011 0.001 PHE J1319 TRP 0.017 0.001 TRP I 997 HIS 0.007 0.001 HIS L 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (32188) covalent geometry : angle 0.54598 / 0.29 (43961) hydrogen bonds : bond 0.03475 / 2.28 ( 1453) hydrogen bonds : angle 3.88469 / 2.70 ( 4002) metal coordination : bond 0.00345 / 0.19 ( 8) metal coordination : angle 2.18140 / 1.26 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15330.67 seconds wall clock time: 259 minutes 58.03 seconds (15598.03 seconds total)