Starting phenix.real_space_refine on Sat Aug 8 23:06:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8to8_41439/08_2026/8to8_41439.cif Found real_map, /net/cci-nas-00/data/ceres_data/8to8_41439/08_2026/8to8_41439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8to8_41439/08_2026/8to8_41439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8to8_41439/08_2026/8to8_41439.map" model { file = "/net/cci-nas-00/data/ceres_data/8to8_41439/08_2026/8to8_41439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8to8_41439/08_2026/8to8_41439.cif" } resolution = 2.9 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= 0.003 sd= 0.069 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 73 5.49 5 Mg 1 5.21 5 S 130 5.16 5 C 19319 2.51 5 N 5506 2.21 5 O 6100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 31131 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1772 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 222} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1684 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 10513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10513 Classifications: {'peptide': 1337} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1279} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "J" Number of atoms: 10382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10382 Classifications: {'peptide': 1336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "L" Number of atoms: 3999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3999 Classifications: {'peptide': 513} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 42} Link IDs: {'PTRANS': 13, 'TRANS': 499} Chain breaks: 4 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 3, 'GLU:plan': 9, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 114 Chain: "M" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "O" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 798 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 2 Chain: "P" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "I" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'4QM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '4QM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'4QM': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14418 SG CYS J 70 102.339 68.331 74.710 1.00 57.45 S ATOM 14432 SG CYS J 72 100.692 66.391 73.118 1.00 68.94 S ATOM 14540 SG CYS J 85 104.060 66.589 72.218 1.00 74.84 S ATOM 14564 SG CYS J 88 100.279 69.056 71.866 1.00 78.91 S ATOM 20252 SG CYS J 814 131.482 119.244 110.564 1.00 50.42 S ATOM 20817 SG CYS J 888 127.788 118.289 108.987 1.00 36.11 S ATOM 20868 SG CYS J 895 129.177 116.861 112.093 1.00 39.63 S ATOM 20889 SG CYS J 898 128.736 119.847 112.414 1.00 42.60 S Time building chain proxies: 6.38, per 1000 atoms: 0.20 Number of scatterers: 31131 At special positions: 0 Unit cell: (153.608, 195.808, 196.652, 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 130 16.00 P 73 15.00 Mg 1 11.99 O 6100 8.00 N 5506 7.00 C 19319 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: 3.07 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " Number of angles added : 12 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7030 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 45 sheets defined 43.1% alpha, 14.5% beta 32 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 4.11 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.789A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.934A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 212 through 233 removed outlier: 3.973A pdb=" N ASP G 233 " --> pdb=" O GLU G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.681A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 87 removed outlier: 3.538A 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 228 Processing helix chain 'I' and resid 29 through 39 Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.885A 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 270 through 281 Processing helix chain 'I' and resid 288 through 293 removed outlier: 4.068A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 293' Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 removed outlier: 4.061A pdb=" N GLU I 382 " --> pdb=" O ARG I 378 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER I 383 " --> pdb=" O GLU I 379 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 480 removed outlier: 4.183A pdb=" N GLU I 461 " --> pdb=" O GLY I 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.489A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) removed outlier: 3.688A 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 removed outlier: 3.877A pdb=" N ALA I 543 " --> pdb=" O ARG I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.613A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 3.588A 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: 3.585A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE I 668 " --> pdb=" O ALA I 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 664 through 668' Processing helix chain 'I' and resid 670 through 674 removed outlier: 3.548A pdb=" N HIS I 673 " --> pdb=" O PHE I 670 " (cutoff:3.500A) Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 713 removed outlier: 4.164A pdb=" N GLY I 713 " --> pdb=" O ALA I 709 " (cutoff:3.500A) Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.715A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 738 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 898 through 907 Processing helix chain 'I' and resid 942 through 979 Processing helix chain 'I' and resid 993 through 1000 removed outlier: 4.118A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1037 removed outlier: 3.612A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.520A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1106' Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.511A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.606A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.793A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 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 1309 removed outlier: 4.137A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.760A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU I1333 " --> pdb=" O GLU I1329 " (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 94 through 100 Processing helix chain 'J' and resid 114 through 117 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 162 through 170 removed outlier: 3.547A pdb=" N GLU J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 207 removed outlier: 3.660A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 231 removed outlier: 3.951A pdb=" N GLY J 231 " --> pdb=" O PHE J 227 " (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 263 through 283 removed outlier: 4.269A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 417 removed outlier: 4.040A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 452 No H-bonds generated for 'chain 'J' and resid 450 through 452' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 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 597 through 612 removed outlier: 3.843A pdb=" N ILE J 601 " --> pdb=" O GLY J 597 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER J 602 " --> pdb=" O LYS J 598 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.650A 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 removed outlier: 4.202A pdb=" N ASN J 680 " --> pdb=" O GLY J 676 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.678A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY J 794 " --> pdb=" O THR J 790 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.820A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 895 through 900 Processing helix chain 'J' and resid 914 through 925 removed outlier: 3.860A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1137 through 1146 removed outlier: 3.570A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1224 removed outlier: 3.586A pdb=" N ILE J1220 " --> pdb=" O ALA J1216 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU J1221 " --> pdb=" O PRO J1217 " (cutoff:3.500A) Processing helix chain 'J' and resid 1225 through 1237 removed outlier: 3.654A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) Processing helix chain 'J' and resid 1237 through 1244 removed outlier: 3.514A pdb=" N TYR J1241 " --> pdb=" O VAL J1237 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 removed outlier: 3.733A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN J1259 " --> pdb=" O VAL J1255 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.513A pdb=" N ALA J1323 " --> pdb=" O PHE J1319 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER J1324 " --> pdb=" O ILE J1320 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE J1325 " --> pdb=" O SER J1321 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1338 Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 3.874A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL J1351 " --> pdb=" O LEU J1347 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE J1352 " --> pdb=" O LYS J1348 " (cutoff:3.500A) Processing helix chain 'J' and resid 1362 through 1375 Processing helix chain 'K' and resid 7 through 14 Processing helix chain 'K' and resid 15 through 32 removed outlier: 3.616A pdb=" N VAL K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 60 through 76 Processing helix chain 'L' and resid 8 through 20 Processing helix chain 'L' and resid 23 through 31 Processing helix chain 'L' and resid 39 through 49 Processing helix chain 'L' and resid 78 through 83 Processing helix chain 'L' and resid 96 through 107 removed outlier: 3.756A pdb=" N THR L 107 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 135 removed outlier: 3.516A pdb=" N GLU L 116 " --> pdb=" O THR L 112 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE L 117 " --> pdb=" O ARG L 113 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP L 118 " --> pdb=" O GLU L 114 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE L 119 " --> pdb=" O GLY L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 153 removed outlier: 4.371A pdb=" N ILE L 141 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR L 142 " --> pdb=" O PRO L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 162 removed outlier: 3.638A pdb=" N LEU L 161 " --> pdb=" O ARG L 157 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE L 162 " --> pdb=" O LEU L 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 157 through 162' Processing helix chain 'L' and resid 217 through 233 removed outlier: 3.642A pdb=" N ASP L 233 " --> pdb=" O VAL L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 258 removed outlier: 3.792A pdb=" N GLN L 246 " --> pdb=" O HIS L 242 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU L 247 " --> pdb=" O ALA L 243 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN L 258 " --> pdb=" O GLU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 292 Processing helix chain 'L' and resid 298 through 307 Processing helix chain 'L' and resid 317 through 322 removed outlier: 3.857A pdb=" N ALA L 321 " --> pdb=" O ALA L 318 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 330 Processing helix chain 'L' and resid 333 through 352 removed outlier: 3.623A pdb=" N GLU L 350 " --> pdb=" O GLN L 346 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 391 removed outlier: 4.788A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 418 Processing helix chain 'L' and resid 426 through 431 removed outlier: 3.795A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) Processing helix chain 'L' and resid 431 through 446 Processing helix chain 'L' and resid 453 through 475 Processing helix chain 'L' and resid 479 through 488 Processing helix chain 'L' and resid 492 through 499 Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.505A pdb=" N PHE L 522 " --> pdb=" O LEU L 519 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 549 removed outlier: 3.554A pdb=" N ALA L 549 " --> pdb=" O HIS L 545 " (cutoff:3.500A) Processing helix chain 'L' and resid 552 through 563 Processing helix chain 'L' and resid 572 through 581 Processing helix chain 'L' and resid 585 through 600 removed outlier: 3.741A pdb=" N HIS L 600 " --> pdb=" O ARG L 596 " (cutoff:3.500A) Processing helix chain 'L' and resid 605 through 612 removed outlier: 3.551A pdb=" N ASP L 612 " --> pdb=" O ARG L 608 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 261 Processing helix chain 'M' and resid 263 through 274 Processing helix chain 'M' and resid 277 through 283 removed outlier: 3.560A pdb=" N LEU M 281 " --> pdb=" O TYR M 277 " (cutoff:3.500A) Processing helix chain 'M' and resid 285 through 291 Processing helix chain 'M' and resid 296 through 310 Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 15 removed outlier: 7.128A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.557A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N SER G 141 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE G 61 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.321A pdb=" N GLY G 108 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N HIS G 132 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL G 110 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 14 through 20 removed outlier: 3.544A pdb=" N THR H 27 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 14 through 20 removed outlier: 3.544A pdb=" N THR H 27 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N HIS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU H 29 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU H 201 " --> pdb=" O GLU H 29 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 97 through 105 removed outlier: 7.519A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 109 through 111 removed outlier: 3.851A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.771A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.752A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLU I 106 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL I 114 " --> pdb=" O GLU I 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.501A pdb=" N SER I 147 " --> pdb=" O ARG I 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 154 through 159 removed outlier: 3.767A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP I 185 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 226 through 229 removed outlier: 4.266A pdb=" N GLU I 226 " --> pdb=" O PHE I 337 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 238 through 239 Processing sheet with id=AB9, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.662A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 301 through 303 removed outlier: 7.494A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.432A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC4, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.357A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 748 through 752 removed outlier: 3.526A pdb=" N ARG I 731 " --> pdb=" O ASP I 728 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.095A pdb=" N ILE I 816 " --> pdb=" O LYS I1078 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ASN I1080 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL I 818 " --> pdb=" O ASN I1080 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.623A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP I 842 " --> pdb=" O VAL I1046 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL I1046 " --> pdb=" O ASP I 842 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 849 through 850 Processing sheet with id=AD2, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.854A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'I' and resid 1268 through 1270 removed outlier: 3.654A pdb=" N GLN I1268 " --> pdb=" O VAL J 347 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 1335 through 1338 Processing sheet with id=AD6, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.623A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 9.936A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.524A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 159 through 161 Processing sheet with id=AD8, first strand: chain 'J' and resid 252 through 254 removed outlier: 6.813A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 526 through 527 removed outlier: 3.648A pdb=" N ARG J 551 " --> pdb=" O LEU J 527 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 703 through 706 Processing sheet with id=AE2, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'J' and resid 825 through 826 removed outlier: 3.899A pdb=" N GLU J 833 " --> pdb=" O VAL J 825 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 949 through 950 removed outlier: 3.955A pdb=" N ILE J 950 " --> pdb=" O ALA J1018 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL J 966 " --> pdb=" O VAL J 974 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.551A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 3.709A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE J1080 " --> pdb=" O VAL J1088 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.547A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER J1058 " --> pdb=" O GLN J1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AE9, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.301A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL J1267 " --> pdb=" O THR J1301 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1317 hydrogen bonds defined for protein. 3723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 8.70 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10354 1.34 - 1.46: 6331 1.46 - 1.58: 14662 1.58 - 1.70: 154 1.70 - 1.83: 240 Bond restraints: 31741 Sorted by residual: bond pdb=" C19 4QM L 701 " pdb=" C3 4QM L 701 " ideal model delta sigma weight residual 1.532 1.826 -0.294 2.00e-02 2.50e+03 2.16e+02 bond pdb=" C19 4QM J1504 " pdb=" C3 4QM J1504 " ideal model delta sigma weight residual 1.532 1.825 -0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C19 4QM I1402 " pdb=" C3 4QM I1402 " ideal model delta sigma weight residual 1.532 1.824 -0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C19 4QM I1401 " pdb=" C3 4QM I1401 " ideal model delta sigma weight residual 1.532 1.823 -0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" C3 4QM J1504 " pdb=" C4 4QM J1504 " ideal model delta sigma weight residual 1.533 1.734 -0.201 2.00e-02 2.50e+03 1.01e+02 ... (remaining 31736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 42584 2.27 - 4.53: 575 4.53 - 6.80: 31 6.80 - 9.06: 11 9.06 - 11.33: 1 Bond angle restraints: 43202 Sorted by residual: angle pdb=" C ILE J 707 " pdb=" N ASN J 708 " pdb=" CA ASN J 708 " ideal model delta sigma weight residual 121.70 133.03 -11.33 1.80e+00 3.09e-01 3.96e+01 angle pdb=" C TYR L 425 " pdb=" CA TYR L 425 " pdb=" CB TYR L 425 " ideal model delta sigma weight residual 110.06 103.73 6.33 1.39e+00 5.18e-01 2.07e+01 angle pdb=" C LYS L 502 " pdb=" CA LYS L 502 " pdb=" CB LYS L 502 " ideal model delta sigma weight residual 117.23 111.05 6.18 1.36e+00 5.41e-01 2.07e+01 angle pdb=" N3 DT O 60 " pdb=" C4 DT O 60 " pdb=" O4 DT O 60 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT O 61 " pdb=" C4 DT O 61 " pdb=" O4 DT O 61 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 ... (remaining 43197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 19100 35.95 - 71.89: 459 71.89 - 107.84: 14 107.84 - 143.78: 1 143.78 - 179.73: 2 Dihedral angle restraints: 19576 sinusoidal: 8681 harmonic: 10895 Sorted by residual: dihedral pdb=" CA TRP I 807 " pdb=" C TRP I 807 " pdb=" N ASN I 808 " pdb=" CA ASN I 808 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA LYS L 236 " pdb=" C LYS L 236 " pdb=" N HIS L 242 " pdb=" CA HIS L 242 " ideal model delta harmonic sigma weight residual -180.00 -154.86 -25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA THR L 583 " pdb=" C THR L 583 " pdb=" N ARG L 584 " pdb=" CA ARG L 584 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 19573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4471 0.077 - 0.155: 477 0.155 - 0.232: 18 0.232 - 0.310: 5 0.310 - 0.387: 8 Chirality restraints: 4979 Sorted by residual: chirality pdb=" C15 4QM J1504 " pdb=" C14 4QM J1504 " pdb=" C16 4QM J1504 " pdb=" C2 4QM J1504 " both_signs ideal model delta sigma weight residual False -2.46 -2.85 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" C19 4QM I1402 " pdb=" C18 4QM I1402 " pdb=" C2 4QM I1402 " pdb=" C3 4QM I1402 " both_signs ideal model delta sigma weight residual False -2.57 -2.96 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C19 4QM L 701 " pdb=" C18 4QM L 701 " pdb=" C2 4QM L 701 " pdb=" C3 4QM L 701 " both_signs ideal model delta sigma weight residual False -2.57 -2.95 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 4976 not shown) Planarity restraints: 5363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 373 " -0.540 9.50e-02 1.11e+02 2.42e-01 3.58e+01 pdb=" NE ARG L 373 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG L 373 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG L 373 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG L 373 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 422 " 0.330 9.50e-02 1.11e+02 1.48e-01 1.34e+01 pdb=" NE ARG L 422 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG L 422 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG L 422 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG L 422 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG I1223 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO I1224 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO I1224 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO I1224 " -0.030 5.00e-02 4.00e+02 ... (remaining 5360 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 201 2.53 - 3.12: 24189 3.12 - 3.72: 45590 3.72 - 4.31: 64329 4.31 - 4.90: 110763 Nonbonded interactions: 245072 Sorted by model distance: nonbonded pdb=" OG1 THR I 91 " pdb=" O ILE I 138 " model vdw 1.941 3.040 nonbonded pdb=" OG SER I 348 " pdb=" OE1 GLU I 349 " model vdw 2.042 3.040 nonbonded pdb=" OH TYR J1186 " pdb=" OE1 GLU J1188 " model vdw 2.064 3.040 nonbonded pdb=" OG SER I 318 " pdb=" OD1 ASP I 320 " model vdw 2.071 3.040 nonbonded pdb=" OH TYR I 179 " pdb=" OE2 GLU I 458 " model vdw 2.091 3.040 ... (remaining 245067 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 5 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 66 or (resid 67 and (name N or name \ CA or name C or name O or name CB )) or resid 68 through 158 or resid 170 throu \ gh 233)) selection = (chain 'H' and (resid 5 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 or (resid 193 through 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 228 or (resid 22 \ 9 through 230 and (name N or name CA or name C or name O or name CB )) or resid \ 231 through 233)) } 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: 3.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 37.830 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.080 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:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 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 : 0.007 0.294 31749 Z= 0.368 Angle : 0.727 46.782 43214 Z= 0.395 Chirality : 0.049 0.387 4979 Planarity : 0.006 0.242 5363 Dihedral : 14.057 179.727 12546 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.49 % Favored : 94.43 % Rotamer: Outliers : 3.49 % Allowed : 6.07 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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: -0.38 (0.14), residues: 3755 helix: 1.29 (0.14), residues: 1486 sheet: -0.91 (0.24), residues: 449 loop : -1.42 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 422 TYR 0.017 0.001 TYR G 177 PHE 0.011 0.001 PHE I 35 TRP 0.010 0.001 TRP I 807 HIS 0.004 0.001 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.37 (31741) covalent geometry : angle 0.63462 / 0.39 (43202) hydrogen bonds : bond 0.15766 / 10.90 ( 1390) hydrogen bonds : angle 6.05113 / 4.22 ( 3881) metal coordination : bond 0.05894 / 3.50 ( 8) metal coordination : angle 21.30530 / 13.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 523 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 ARG cc_start: 0.7399 (ptm-80) cc_final: 0.7096 (mtp-110) REVERT: G 57 THR cc_start: 0.8966 (m) cc_final: 0.8707 (p) REVERT: G 170 ARG cc_start: 0.7823 (ttp-170) cc_final: 0.7623 (ttp-170) REVERT: H 111 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7423 (m) REVERT: I 40 GLU cc_start: 0.7617 (tp30) cc_final: 0.7416 (tt0) REVERT: I 161 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7355 (mmtt) REVERT: I 183 TRP cc_start: 0.8018 (m-10) cc_final: 0.7606 (m-10) REVERT: I 263 VAL cc_start: 0.6322 (OUTLIER) cc_final: 0.6090 (t) REVERT: I 503 LYS cc_start: 0.7834 (tptm) cc_final: 0.7336 (ptmt) REVERT: I 587 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8847 (mt) REVERT: I 633 LEU cc_start: 0.8010 (mp) cc_final: 0.7780 (mp) REVERT: I 699 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8576 (mp) REVERT: I 866 ASP cc_start: 0.8549 (p0) cc_final: 0.8128 (p0) REVERT: I 912 ASP cc_start: 0.5553 (OUTLIER) cc_final: 0.5205 (p0) REVERT: I 955 GLN cc_start: 0.7578 (tp40) cc_final: 0.7326 (tm-30) REVERT: I 958 LYS cc_start: 0.7826 (ttmm) cc_final: 0.7626 (ttpp) REVERT: I 1171 ARG cc_start: 0.8353 (ttp80) cc_final: 0.8113 (ttp-170) REVERT: J 79 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7622 (ptpp) REVERT: J 129 ASP cc_start: 0.7775 (t0) cc_final: 0.7390 (t0) REVERT: J 219 LYS cc_start: 0.7271 (mtpp) cc_final: 0.6996 (tppp) REVERT: J 549 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8289 (mttm) REVERT: J 695 LYS cc_start: 0.8033 (ttpp) cc_final: 0.7725 (ttmm) REVERT: J 705 THR cc_start: 0.9049 (p) cc_final: 0.8793 (t) REVERT: J 740 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8610 (mt) REVERT: J 833 GLU cc_start: 0.8252 (tt0) cc_final: 0.8042 (tt0) REVERT: J 874 GLU cc_start: 0.7222 (tt0) cc_final: 0.6875 (pt0) REVERT: J 1305 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.7081 (m-30) REVERT: J 1368 ASP cc_start: 0.8023 (t0) cc_final: 0.7776 (m-30) REVERT: L 561 MET cc_start: 0.7793 (tpt) cc_final: 0.7426 (mmm) REVERT: L 575 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7993 (mp0) outliers start: 111 outliers final: 35 residues processed: 616 average time/residue: 0.7699 time to fit residues: 553.0714 Evaluate side-chains 412 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 367 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 327 GLN Chi-restraints excluded: chain I residue 349 GLU Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 475 VAL Chi-restraints excluded: chain I residue 519 ASN Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 768 ASN Chi-restraints excluded: chain J residue 897 HIS Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain L residue 346 GLN Chi-restraints excluded: chain L residue 423 ARG Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 469 GLN Chi-restraints excluded: chain L residue 575 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 75 GLN I 343 HIS I 387 ASN I 604 HIS I 811 ASN I1136 GLN J 777 HIS J1238 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.212269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128345 restraints weight = 33795.507| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.38 r_work: 0.3242 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31749 Z= 0.151 Angle : 0.635 13.025 43214 Z= 0.334 Chirality : 0.044 0.248 4979 Planarity : 0.005 0.073 5363 Dihedral : 14.100 177.787 5293 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.85 % Favored : 95.07 % Rotamer: Outliers : 3.46 % Allowed : 12.74 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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: -0.10 (0.14), residues: 3755 helix: 1.50 (0.14), residues: 1504 sheet: -0.82 (0.24), residues: 431 loop : -1.25 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 378 TYR 0.017 0.001 TYR G 177 PHE 0.025 0.002 PHE L 427 TRP 0.020 0.001 TRP L 326 HIS 0.005 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (31741) covalent geometry : angle 0.62950 / 0.33 (43202) hydrogen bonds : bond 0.05039 / 3.36 ( 1390) hydrogen bonds : angle 4.73078 / 3.26 ( 3881) metal coordination : bond 0.01396 / 0.74 ( 8) metal coordination : angle 5.14536 / 3.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 382 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 ARG cc_start: 0.7470 (ptm-80) cc_final: 0.7106 (mtp-110) REVERT: G 57 THR cc_start: 0.8934 (m) cc_final: 0.8694 (p) REVERT: G 170 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7824 (ttp-170) REVERT: G 233 ASP cc_start: 0.6318 (OUTLIER) cc_final: 0.5823 (p0) REVERT: H 96 ASP cc_start: 0.7265 (m-30) cc_final: 0.7026 (p0) REVERT: H 193 GLU cc_start: 0.7912 (pp20) cc_final: 0.7669 (pp20) REVERT: I 20 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7226 (mt0) REVERT: I 40 GLU cc_start: 0.7769 (tp30) cc_final: 0.7549 (mt-10) REVERT: I 161 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7700 (mmtt) REVERT: I 175 ARG cc_start: 0.7971 (ttm170) cc_final: 0.7692 (mtp85) REVERT: I 183 TRP cc_start: 0.8244 (m-10) cc_final: 0.7742 (m-10) REVERT: I 394 ARG cc_start: 0.8175 (tpp80) cc_final: 0.7837 (tpp-160) REVERT: I 488 MET cc_start: 0.7387 (mmm) cc_final: 0.7147 (mmm) REVERT: I 503 LYS cc_start: 0.7636 (tptm) cc_final: 0.6860 (ptmt) REVERT: I 587 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8692 (mt) REVERT: I 672 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8011 (pm20) REVERT: I 697 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.7849 (pttm) REVERT: I 866 ASP cc_start: 0.8260 (p0) cc_final: 0.7942 (p0) REVERT: I 902 LEU cc_start: 0.7723 (tt) cc_final: 0.7375 (tp) REVERT: I 925 SER cc_start: 0.8785 (p) cc_final: 0.8375 (m) REVERT: I 958 LYS cc_start: 0.7568 (ttmm) cc_final: 0.7320 (ttpp) REVERT: I 1089 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7495 (pm20) REVERT: I 1140 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7735 (mttp) REVERT: J 66 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.7025 (ptmm) REVERT: J 76 LYS cc_start: 0.8177 (pttt) cc_final: 0.7792 (ttpp) REVERT: J 79 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7464 (ptpp) REVERT: J 84 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8612 (mm) REVERT: J 129 ASP cc_start: 0.7908 (t0) cc_final: 0.7513 (t0) REVERT: J 130 MET cc_start: 0.7468 (tpt) cc_final: 0.6977 (ttp) REVERT: J 144 TYR cc_start: 0.7132 (m-80) cc_final: 0.6815 (m-80) REVERT: J 158 GLN cc_start: 0.6918 (tt0) cc_final: 0.6201 (mt0) REVERT: J 695 LYS cc_start: 0.7822 (ttpp) cc_final: 0.7401 (ttmm) REVERT: J 705 THR cc_start: 0.9073 (p) cc_final: 0.8747 (t) REVERT: J 740 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8329 (mt) REVERT: J 795 TYR cc_start: 0.8267 (t80) cc_final: 0.7587 (t80) REVERT: J 874 GLU cc_start: 0.7548 (tt0) cc_final: 0.7285 (tt0) REVERT: J 1305 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7402 (m-30) REVERT: J 1317 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6173 (pp20) REVERT: J 1361 THR cc_start: 0.8951 (m) cc_final: 0.8611 (p) REVERT: J 1368 ASP cc_start: 0.7925 (t0) cc_final: 0.7371 (m-30) REVERT: L 100 MET cc_start: 0.6141 (mtp) cc_final: 0.5922 (mpp) REVERT: L 322 MET cc_start: -0.0024 (OUTLIER) cc_final: -0.0957 (pp-130) REVERT: L 379 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7824 (ttp) REVERT: L 392 LYS cc_start: 0.8090 (mtpt) cc_final: 0.7853 (mppt) REVERT: L 430 TYR cc_start: 0.8455 (t80) cc_final: 0.8253 (t80) REVERT: L 561 MET cc_start: 0.7927 (tpt) cc_final: 0.7604 (mmm) REVERT: L 578 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8625 (pttm) REVERT: L 586 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7071 (tpt90) REVERT: L 589 GLN cc_start: 0.8848 (mt0) cc_final: 0.8380 (mt0) REVERT: M 316 MET cc_start: 0.8343 (pmm) cc_final: 0.7995 (pmm) outliers start: 110 outliers final: 38 residues processed: 459 average time/residue: 0.6069 time to fit residues: 329.2710 Evaluate side-chains 401 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 345 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 161 LYS Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 327 GLN Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1089 GLU Chi-restraints excluded: chain I residue 1140 LYS Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 1293 GLU Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1317 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain L residue 322 MET Chi-restraints excluded: chain L residue 379 MET Chi-restraints excluded: chain L residue 423 ARG Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 578 LYS Chi-restraints excluded: chain L residue 586 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 285 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 258 optimal weight: 10.0000 chunk 311 optimal weight: 4.9990 chunk 332 optimal weight: 40.0000 chunk 226 optimal weight: 0.7980 chunk 319 optimal weight: 50.0000 chunk 44 optimal weight: 5.9990 chunk 268 optimal weight: 0.0370 chunk 118 optimal weight: 4.9990 overall best weight: 2.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 343 HIS I 510 GLN I 628 HIS I 811 ASN I 932 GLN J1326 GLN L 147 GLN L 265 GLN L 345 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.209924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118987 restraints weight = 33455.891| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.27 r_work: 0.3134 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 31749 Z= 0.273 Angle : 0.698 11.992 43214 Z= 0.362 Chirality : 0.048 0.293 4979 Planarity : 0.006 0.083 5363 Dihedral : 13.817 177.244 5252 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.35 % Favored : 94.59 % Rotamer: Outliers : 5.22 % Allowed : 12.70 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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: -0.43 (0.13), residues: 3755 helix: 1.18 (0.13), residues: 1518 sheet: -0.98 (0.23), residues: 439 loop : -1.41 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 388 TYR 0.031 0.002 TYR G 177 PHE 0.021 0.002 PHE I 405 TRP 0.028 0.002 TRP L 326 HIS 0.008 0.002 HIS J 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.27 (31741) covalent geometry : angle 0.69476 / 0.36 (43202) hydrogen bonds : bond 0.05724 / 3.88 ( 1390) hydrogen bonds : angle 4.64908 / 3.20 ( 3881) metal coordination : bond 0.01555 / 0.84 ( 8) metal coordination : angle 4.34747 / 2.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 363 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 ARG cc_start: 0.7544 (ptm-80) cc_final: 0.6796 (mtt180) REVERT: G 72 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: G 195 ARG cc_start: 0.7297 (mtp180) cc_final: 0.7087 (mtp180) REVERT: G 233 ASP cc_start: 0.6464 (OUTLIER) cc_final: 0.5992 (p0) REVERT: H 96 ASP cc_start: 0.7313 (m-30) cc_final: 0.7041 (p0) REVERT: H 110 VAL cc_start: 0.8611 (t) cc_final: 0.8248 (p) REVERT: H 193 GLU cc_start: 0.8116 (pp20) cc_final: 0.7815 (pp20) REVERT: I 20 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7308 (mt0) REVERT: I 40 GLU cc_start: 0.8025 (tp30) cc_final: 0.7723 (mt-10) REVERT: I 72 SER cc_start: 0.7914 (t) cc_final: 0.7411 (m) REVERT: I 175 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7875 (mtp85) REVERT: I 183 TRP cc_start: 0.8272 (m-10) cc_final: 0.7735 (m-10) REVERT: I 503 LYS cc_start: 0.7719 (tptm) cc_final: 0.6790 (ptmt) REVERT: I 672 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: I 866 ASP cc_start: 0.8401 (p0) cc_final: 0.8060 (p0) REVERT: I 902 LEU cc_start: 0.7931 (tt) cc_final: 0.7634 (tp) REVERT: I 955 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7323 (tm-30) REVERT: I 958 LYS cc_start: 0.7611 (ttmm) cc_final: 0.7354 (ttpp) REVERT: J 66 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7272 (ptmm) REVERT: J 76 LYS cc_start: 0.8382 (pttt) cc_final: 0.7960 (ttpp) REVERT: J 79 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7409 (ptpp) REVERT: J 84 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8695 (mm) REVERT: J 94 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8033 (mt0) REVERT: J 129 ASP cc_start: 0.7927 (t0) cc_final: 0.7490 (t0) REVERT: J 158 GLN cc_start: 0.6952 (tt0) cc_final: 0.6288 (mt0) REVERT: J 321 LYS cc_start: 0.8676 (mmmt) cc_final: 0.8459 (mmmm) REVERT: J 362 ARG cc_start: 0.8838 (mtm180) cc_final: 0.8538 (mtp180) REVERT: J 556 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7335 (tp30) REVERT: J 695 LYS cc_start: 0.7941 (ttpp) cc_final: 0.7540 (ttmm) REVERT: J 705 THR cc_start: 0.9062 (p) cc_final: 0.8732 (t) REVERT: J 740 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8521 (mt) REVERT: J 874 GLU cc_start: 0.7600 (tt0) cc_final: 0.7331 (tt0) REVERT: J 1152 GLU cc_start: 0.8118 (mp0) cc_final: 0.7815 (tm-30) REVERT: J 1249 ASN cc_start: 0.8992 (OUTLIER) cc_final: 0.8576 (t0) REVERT: J 1276 GLU cc_start: 0.7315 (tm-30) cc_final: 0.7077 (tm-30) REVERT: J 1305 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7524 (m-30) REVERT: J 1317 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6576 (pp20) REVERT: J 1368 ASP cc_start: 0.8015 (t0) cc_final: 0.7389 (m-30) REVERT: L 100 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.5996 (mpp) REVERT: L 297 MET cc_start: -0.0857 (pp-130) cc_final: -0.1198 (ppp) REVERT: L 322 MET cc_start: -0.0688 (OUTLIER) cc_final: -0.1891 (pp-130) REVERT: L 365 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8949 (mpp) REVERT: L 392 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7911 (mppt) REVERT: L 555 GLU cc_start: 0.8228 (mp0) cc_final: 0.7982 (mp0) REVERT: L 561 MET cc_start: 0.8085 (tpt) cc_final: 0.7810 (mmm) REVERT: L 589 GLN cc_start: 0.8854 (mt0) cc_final: 0.8495 (mt0) REVERT: M 316 MET cc_start: 0.8386 (pmm) cc_final: 0.8072 (pmm) outliers start: 166 outliers final: 83 residues processed: 477 average time/residue: 0.6477 time to fit residues: 368.1268 Evaluate side-chains 446 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 347 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 197 ASP Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 327 GLN Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 854 ILE Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 954 LYS Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 556 GLU Chi-restraints excluded: chain J residue 663 GLU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1293 GLU Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1317 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 128 ASN Chi-restraints excluded: chain L residue 322 MET Chi-restraints excluded: chain L residue 365 MET Chi-restraints excluded: chain L residue 381 GLU Chi-restraints excluded: chain L residue 423 ARG Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 578 LYS Chi-restraints excluded: chain L residue 586 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 364 optimal weight: 9.9990 chunk 316 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 203 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 343 optimal weight: 30.0000 chunk 217 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 343 HIS I 811 ASN J 777 HIS J1244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.211338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122527 restraints weight = 33441.823| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.10 r_work: 0.3198 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31749 Z= 0.147 Angle : 0.590 15.555 43214 Z= 0.310 Chirality : 0.043 0.265 4979 Planarity : 0.005 0.064 5363 Dihedral : 13.728 177.467 5248 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.74 % Favored : 95.21 % Rotamer: Outliers : 4.21 % Allowed : 14.53 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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: -0.18 (0.14), residues: 3755 helix: 1.43 (0.14), residues: 1516 sheet: -0.81 (0.24), residues: 423 loop : -1.32 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 388 TYR 0.026 0.001 TYR L 148 PHE 0.028 0.001 PHE L 427 TRP 0.027 0.001 TRP L 326 HIS 0.006 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (31741) covalent geometry : angle 0.58715 / 0.31 (43202) hydrogen bonds : bond 0.04467 / 3.01 ( 1390) hydrogen bonds : angle 4.42833 / 3.04 ( 3881) metal coordination : bond 0.00684 / 0.38 ( 8) metal coordination : angle 3.79471 / 2.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 365 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 ARG cc_start: 0.7454 (ptm-80) cc_final: 0.6730 (mtt180) REVERT: G 67 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8497 (pt0) REVERT: G 195 ARG cc_start: 0.7148 (mtp180) cc_final: 0.6925 (mtp180) REVERT: G 233 ASP cc_start: 0.6213 (OUTLIER) cc_final: 0.5772 (p0) REVERT: H 76 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: H 96 ASP cc_start: 0.7251 (m-30) cc_final: 0.6976 (p0) REVERT: H 110 VAL cc_start: 0.8596 (t) cc_final: 0.8219 (p) REVERT: H 111 THR cc_start: 0.7008 (OUTLIER) cc_final: 0.6633 (t) REVERT: H 114 ASP cc_start: 0.7163 (m-30) cc_final: 0.6871 (m-30) REVERT: H 193 GLU cc_start: 0.8039 (pp20) cc_final: 0.7719 (pp20) REVERT: I 20 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7269 (mt0) REVERT: I 40 GLU cc_start: 0.7814 (tp30) cc_final: 0.7563 (mt-10) REVERT: I 72 SER cc_start: 0.7848 (t) cc_final: 0.7347 (m) REVERT: I 142 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8780 (mt-10) REVERT: I 175 ARG cc_start: 0.8021 (ttm170) cc_final: 0.7777 (mtp85) REVERT: I 183 TRP cc_start: 0.8151 (m-10) cc_final: 0.7611 (m-10) REVERT: I 343 HIS cc_start: 0.5572 (OUTLIER) cc_final: 0.5357 (m90) REVERT: I 394 ARG cc_start: 0.8234 (tpp80) cc_final: 0.7962 (tpp80) REVERT: I 488 MET cc_start: 0.7362 (mmm) cc_final: 0.7141 (mmm) REVERT: I 503 LYS cc_start: 0.7624 (tptm) cc_final: 0.6732 (ptmt) REVERT: I 516 ASP cc_start: 0.8500 (m-30) cc_final: 0.8290 (m-30) REVERT: I 631 GLU cc_start: 0.8132 (mm-30) cc_final: 0.6849 (mp0) REVERT: I 672 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7916 (pm20) REVERT: I 866 ASP cc_start: 0.8250 (p0) cc_final: 0.7953 (p0) REVERT: I 902 LEU cc_start: 0.7887 (tt) cc_final: 0.7675 (tp) REVERT: I 925 SER cc_start: 0.8852 (p) cc_final: 0.8396 (m) REVERT: I 955 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7258 (tm-30) REVERT: I 958 LYS cc_start: 0.7526 (ttmm) cc_final: 0.7254 (ttpp) REVERT: I 1140 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7650 (mttp) REVERT: I 1150 ASP cc_start: 0.8370 (p0) cc_final: 0.8119 (m-30) REVERT: I 1290 MET cc_start: 0.9071 (mtt) cc_final: 0.8807 (mmt) REVERT: J 66 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.7060 (ptmm) REVERT: J 76 LYS cc_start: 0.8349 (pttt) cc_final: 0.7996 (ttpp) REVERT: J 79 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7440 (ptpp) REVERT: J 84 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8573 (mm) REVERT: J 94 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: J 129 ASP cc_start: 0.7844 (t0) cc_final: 0.7410 (t0) REVERT: J 158 GLN cc_start: 0.6866 (tt0) cc_final: 0.6224 (mt0) REVERT: J 321 LYS cc_start: 0.8683 (mmmt) cc_final: 0.8446 (mmmm) REVERT: J 695 LYS cc_start: 0.7816 (ttpp) cc_final: 0.7395 (ttmm) REVERT: J 740 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8295 (mt) REVERT: J 874 GLU cc_start: 0.7568 (tt0) cc_final: 0.7321 (tt0) REVERT: J 1152 GLU cc_start: 0.8086 (mp0) cc_final: 0.7822 (tm-30) REVERT: J 1261 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8296 (pp) REVERT: J 1265 THR cc_start: 0.8762 (m) cc_final: 0.8201 (p) REVERT: J 1276 GLU cc_start: 0.7326 (tm-30) cc_final: 0.7121 (tm-30) REVERT: J 1305 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7495 (m-30) REVERT: J 1317 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6452 (pp20) REVERT: J 1361 THR cc_start: 0.8929 (m) cc_final: 0.8572 (p) REVERT: J 1368 ASP cc_start: 0.7915 (t0) cc_final: 0.7315 (m-30) REVERT: J 1370 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.4951 (mpt) REVERT: L 100 MET cc_start: 0.6314 (mtp) cc_final: 0.5986 (mpp) REVERT: L 116 GLU cc_start: 0.8697 (mp0) cc_final: 0.8429 (pm20) REVERT: L 297 MET cc_start: -0.0622 (pp-130) cc_final: -0.0853 (ppp) REVERT: L 425 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.6794 (m-80) REVERT: L 489 MET cc_start: 0.8024 (mtt) cc_final: 0.7507 (mtp) REVERT: L 561 MET cc_start: 0.8220 (tpt) cc_final: 0.7890 (mmm) REVERT: L 567 MET cc_start: 0.8682 (mtp) cc_final: 0.8286 (mtp) REVERT: L 589 GLN cc_start: 0.8876 (mt0) cc_final: 0.8329 (mt0) REVERT: M 316 MET cc_start: 0.8228 (pmm) cc_final: 0.7982 (pmm) outliers start: 134 outliers final: 61 residues processed: 450 average time/residue: 0.6758 time to fit residues: 361.1694 Evaluate side-chains 429 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 349 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 142 GLU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 327 GLN Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 954 LYS Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1140 LYS Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 663 GLU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1293 GLU Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1317 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain L residue 381 GLU Chi-restraints excluded: chain L residue 422 ARG Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 578 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 234 optimal weight: 0.9990 chunk 314 optimal weight: 5.9990 chunk 163 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 139 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 196 optimal weight: 20.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 343 HIS I 620 ASN I 811 ASN J 777 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.211081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.125918 restraints weight = 33704.799| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.10 r_work: 0.3181 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31749 Z= 0.157 Angle : 0.587 11.354 43214 Z= 0.309 Chirality : 0.043 0.274 4979 Planarity : 0.005 0.061 5363 Dihedral : 13.684 177.543 5241 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 4.15 % Allowed : 15.31 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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: -0.14 (0.14), residues: 3755 helix: 1.45 (0.14), residues: 1517 sheet: -0.77 (0.24), residues: 427 loop : -1.30 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 274 TYR 0.029 0.002 TYR L 148 PHE 0.014 0.001 PHE I 405 TRP 0.022 0.001 TRP L 326 HIS 0.005 0.001 HIS I 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (31741) covalent geometry : angle 0.58479 / 0.31 (43202) hydrogen bonds : bond 0.04431 / 2.99 ( 1390) hydrogen bonds : angle 4.38287 / 3.00 ( 3881) metal coordination : bond 0.00749 / 0.41 ( 8) metal coordination : angle 3.38020 / 2.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 355 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 ARG cc_start: 0.7621 (ptm-80) cc_final: 0.6866 (mtt180) REVERT: H 96 ASP cc_start: 0.7234 (m-30) cc_final: 0.7006 (p0) REVERT: H 110 VAL cc_start: 0.8732 (t) cc_final: 0.8365 (p) REVERT: H 111 THR cc_start: 0.6899 (OUTLIER) cc_final: 0.6412 (t) REVERT: H 114 ASP cc_start: 0.7146 (m-30) cc_final: 0.6812 (m-30) REVERT: I 20 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7319 (mt0) REVERT: I 40 GLU cc_start: 0.7798 (tp30) cc_final: 0.7589 (mt-10) REVERT: I 72 SER cc_start: 0.7944 (t) cc_final: 0.7472 (m) REVERT: I 175 ARG cc_start: 0.8051 (ttm170) cc_final: 0.7830 (mtp85) REVERT: I 183 TRP cc_start: 0.8202 (m-10) cc_final: 0.7692 (m-10) REVERT: I 394 ARG cc_start: 0.8302 (tpp80) cc_final: 0.8055 (tpp80) REVERT: I 503 LYS cc_start: 0.7710 (tptm) cc_final: 0.6834 (ptmt) REVERT: I 516 ASP cc_start: 0.8511 (m-30) cc_final: 0.8259 (m-30) REVERT: I 631 GLU cc_start: 0.8154 (mm-30) cc_final: 0.6950 (mp0) REVERT: I 672 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7896 (pm20) REVERT: I 866 ASP cc_start: 0.8347 (p0) cc_final: 0.8018 (p0) REVERT: I 902 LEU cc_start: 0.8107 (tt) cc_final: 0.7893 (tp) REVERT: I 925 SER cc_start: 0.8827 (OUTLIER) cc_final: 0.8392 (m) REVERT: I 955 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7403 (tm-30) REVERT: I 958 LYS cc_start: 0.7601 (ttmm) cc_final: 0.7341 (ttpp) REVERT: I 1140 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7752 (mttp) REVERT: J 66 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7224 (ptmm) REVERT: J 76 LYS cc_start: 0.8456 (pttt) cc_final: 0.8162 (ttpp) REVERT: J 79 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7487 (ptpp) REVERT: J 94 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7994 (mt0) REVERT: J 129 ASP cc_start: 0.7855 (t0) cc_final: 0.7448 (t0) REVERT: J 158 GLN cc_start: 0.6947 (tt0) cc_final: 0.6321 (mt0) REVERT: J 321 LYS cc_start: 0.8689 (mmmt) cc_final: 0.8431 (mmmm) REVERT: J 695 LYS cc_start: 0.7904 (ttpp) cc_final: 0.7513 (ttmm) REVERT: J 740 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8356 (mt) REVERT: J 795 TYR cc_start: 0.8398 (t80) cc_final: 0.7820 (t80) REVERT: J 874 GLU cc_start: 0.7656 (tt0) cc_final: 0.7422 (tt0) REVERT: J 1261 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8330 (pp) REVERT: J 1265 THR cc_start: 0.8808 (m) cc_final: 0.8320 (p) REVERT: J 1305 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: J 1317 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6480 (pp20) REVERT: J 1361 THR cc_start: 0.8946 (m) cc_final: 0.8601 (p) REVERT: J 1368 ASP cc_start: 0.8005 (t0) cc_final: 0.7454 (m-30) REVERT: J 1370 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.5195 (mpt) REVERT: L 100 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.6181 (mpp) REVERT: L 116 GLU cc_start: 0.8597 (mp0) cc_final: 0.8361 (pm20) REVERT: L 256 PHE cc_start: 0.9368 (t80) cc_final: 0.9131 (t80) REVERT: L 567 MET cc_start: 0.8762 (mtp) cc_final: 0.8432 (mtp) REVERT: L 589 GLN cc_start: 0.8809 (mt0) cc_final: 0.8533 (mt0) REVERT: M 316 MET cc_start: 0.8086 (pmm) cc_final: 0.7849 (pmm) outliers start: 132 outliers final: 76 residues processed: 440 average time/residue: 0.6087 time to fit residues: 319.2975 Evaluate side-chains 430 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 340 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 197 ASP Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 327 GLN Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 753 LEU Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 954 LYS Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1140 LYS Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 663 GLU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 1236 GLU Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1293 GLU Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1317 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 278 ASP Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 578 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 7 optimal weight: 0.9990 chunk 121 optimal weight: 0.0020 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 294 optimal weight: 1.9990 chunk 262 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 288 optimal weight: 8.9990 chunk 307 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 343 HIS I 620 ASN I 811 ASN J1244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.211477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136459 restraints weight = 33462.676| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.68 r_work: 0.3276 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31749 Z= 0.137 Angle : 0.570 11.422 43214 Z= 0.300 Chirality : 0.042 0.273 4979 Planarity : 0.004 0.058 5363 Dihedral : 13.686 177.733 5241 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.23 % Rotamer: Outliers : 4.65 % Allowed : 15.41 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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: -0.03 (0.14), residues: 3755 helix: 1.54 (0.14), residues: 1517 sheet: -0.71 (0.24), residues: 432 loop : -1.22 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 388 TYR 0.031 0.001 TYR L 148 PHE 0.013 0.001 PHE I 405 TRP 0.015 0.001 TRP L 326 HIS 0.006 0.001 HIS I 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (31741) covalent geometry : angle 0.56794 / 0.30 (43202) hydrogen bonds : bond 0.04178 / 2.82 ( 1390) hydrogen bonds : angle 4.29252 / 2.94 ( 3881) metal coordination : bond 0.00599 / 0.33 ( 8) metal coordination : angle 3.13614 / 1.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 347 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 ARG cc_start: 0.7569 (ptm-80) cc_final: 0.6966 (mtt180) REVERT: G 170 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7728 (ttp-170) REVERT: H 110 VAL cc_start: 0.8806 (t) cc_final: 0.8477 (p) REVERT: H 111 THR cc_start: 0.6921 (OUTLIER) cc_final: 0.6423 (t) REVERT: H 114 ASP cc_start: 0.7048 (m-30) cc_final: 0.6731 (m-30) REVERT: I 20 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7122 (mt0) REVERT: I 72 SER cc_start: 0.7950 (t) cc_final: 0.7563 (m) REVERT: I 175 ARG cc_start: 0.7979 (ttm170) cc_final: 0.7771 (mtp85) REVERT: I 183 TRP cc_start: 0.8201 (m-10) cc_final: 0.7719 (m-10) REVERT: I 394 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7982 (tpp80) REVERT: I 503 LYS cc_start: 0.7669 (tptm) cc_final: 0.6904 (ptmt) REVERT: I 516 ASP cc_start: 0.8350 (m-30) cc_final: 0.8077 (m-30) REVERT: I 631 GLU cc_start: 0.8045 (mm-30) cc_final: 0.6979 (mp0) REVERT: I 672 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7902 (pm20) REVERT: I 866 ASP cc_start: 0.8301 (p0) cc_final: 0.7939 (p0) REVERT: I 925 SER cc_start: 0.8704 (OUTLIER) cc_final: 0.8279 (m) REVERT: I 955 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7358 (tm-30) REVERT: I 958 LYS cc_start: 0.7685 (ttmm) cc_final: 0.7437 (ttpp) REVERT: I 1140 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7699 (mttp) REVERT: J 66 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7213 (ptmm) REVERT: J 76 LYS cc_start: 0.8464 (pttt) cc_final: 0.8244 (ttpp) REVERT: J 79 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7657 (ptpp) REVERT: J 94 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7844 (mt0) REVERT: J 129 ASP cc_start: 0.7817 (t0) cc_final: 0.7525 (t0) REVERT: J 130 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6675 (tpt) REVERT: J 158 GLN cc_start: 0.7021 (tt0) cc_final: 0.6450 (mt0) REVERT: J 219 LYS cc_start: 0.7320 (mtpp) cc_final: 0.6887 (tppp) REVERT: J 321 LYS cc_start: 0.8693 (mmmt) cc_final: 0.8467 (mmmm) REVERT: J 556 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: J 695 LYS cc_start: 0.7935 (ttpp) cc_final: 0.7559 (ttmm) REVERT: J 740 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8364 (mt) REVERT: J 795 TYR cc_start: 0.8352 (t80) cc_final: 0.7829 (t80) REVERT: J 1244 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7690 (mm-40) REVERT: J 1261 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8302 (pp) REVERT: J 1305 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7571 (m-30) REVERT: J 1317 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6459 (pp20) REVERT: J 1361 THR cc_start: 0.8862 (m) cc_final: 0.8531 (p) REVERT: J 1368 ASP cc_start: 0.8042 (t0) cc_final: 0.7536 (m-30) REVERT: J 1370 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.5281 (mpt) REVERT: L 100 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.6169 (mpp) REVERT: L 116 GLU cc_start: 0.8495 (mp0) cc_final: 0.8281 (pm20) REVERT: L 429 THR cc_start: 0.8547 (m) cc_final: 0.8001 (p) REVERT: L 567 MET cc_start: 0.8889 (mtp) cc_final: 0.8450 (mtp) REVERT: L 589 GLN cc_start: 0.8799 (mt0) cc_final: 0.8488 (mt0) outliers start: 148 outliers final: 75 residues processed: 443 average time/residue: 0.6557 time to fit residues: 346.8958 Evaluate side-chains 426 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 333 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 327 GLN Chi-restraints excluded: chain I residue 338 THR Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 954 LYS Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1140 LYS Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 192 MET Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 556 GLU Chi-restraints excluded: chain J residue 663 GLU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 1236 GLU Chi-restraints excluded: chain J residue 1244 GLN Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1317 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 507 MET Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 571 TYR Chi-restraints excluded: chain L residue 578 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 254 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 chunk 145 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 chunk 378 optimal weight: 50.0000 chunk 149 optimal weight: 0.5980 chunk 356 optimal weight: 3.9990 chunk 232 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 343 HIS I 620 ASN I 811 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.211498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.135366 restraints weight = 33555.593| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.75 r_work: 0.3268 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31749 Z= 0.139 Angle : 0.578 11.679 43214 Z= 0.302 Chirality : 0.042 0.278 4979 Planarity : 0.004 0.058 5363 Dihedral : 13.703 177.868 5241 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.93 % Favored : 95.05 % Rotamer: Outliers : 3.99 % Allowed : 16.51 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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: 0.01 (0.14), residues: 3755 helix: 1.56 (0.14), residues: 1518 sheet: -0.63 (0.24), residues: 432 loop : -1.20 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 388 TYR 0.037 0.002 TYR L 148 PHE 0.029 0.001 PHE L 259 TRP 0.019 0.001 TRP L 326 HIS 0.007 0.001 HIS I 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (31741) covalent geometry : angle 0.57608 / 0.30 (43202) hydrogen bonds : bond 0.04101 / 2.77 ( 1390) hydrogen bonds : angle 4.26179 / 2.92 ( 3881) metal coordination : bond 0.00605 / 0.33 ( 8) metal coordination : angle 3.00295 / 1.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 347 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 ARG cc_start: 0.7597 (ptm-80) cc_final: 0.7001 (mtt180) REVERT: G 170 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7685 (ttp-170) REVERT: H 110 VAL cc_start: 0.8835 (t) cc_final: 0.8526 (p) REVERT: H 111 THR cc_start: 0.6909 (OUTLIER) cc_final: 0.6300 (t) REVERT: H 114 ASP cc_start: 0.7076 (m-30) cc_final: 0.6706 (m-30) REVERT: I 20 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.7142 (mt0) REVERT: I 72 SER cc_start: 0.7959 (t) cc_final: 0.7574 (m) REVERT: I 183 TRP cc_start: 0.8216 (m-10) cc_final: 0.7728 (m-10) REVERT: I 394 ARG cc_start: 0.8232 (tpp80) cc_final: 0.8001 (tpp80) REVERT: I 475 VAL cc_start: 0.6762 (p) cc_final: 0.6543 (p) REVERT: I 503 LYS cc_start: 0.7651 (tptm) cc_final: 0.6919 (ptmt) REVERT: I 516 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8076 (m-30) REVERT: I 631 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7006 (mp0) REVERT: I 672 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7912 (pm20) REVERT: I 866 ASP cc_start: 0.8305 (p0) cc_final: 0.7927 (p0) REVERT: I 925 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8267 (m) REVERT: I 955 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7335 (tm-30) REVERT: I 958 LYS cc_start: 0.7679 (ttmm) cc_final: 0.7442 (ttpp) REVERT: I 1136 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: J 66 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7224 (ptmm) REVERT: J 76 LYS cc_start: 0.8454 (pttt) cc_final: 0.8227 (ttpp) REVERT: J 79 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7607 (ptpp) REVERT: J 94 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7764 (mt0) REVERT: J 129 ASP cc_start: 0.7777 (t0) cc_final: 0.7511 (t0) REVERT: J 130 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6686 (tpt) REVERT: J 158 GLN cc_start: 0.7023 (tt0) cc_final: 0.6458 (mt0) REVERT: J 219 LYS cc_start: 0.7327 (mtpp) cc_final: 0.6901 (tppp) REVERT: J 321 LYS cc_start: 0.8712 (mmmt) cc_final: 0.8494 (mmmm) REVERT: J 545 HIS cc_start: 0.9114 (OUTLIER) cc_final: 0.8844 (m90) REVERT: J 695 LYS cc_start: 0.7948 (ttpp) cc_final: 0.7576 (ttmm) REVERT: J 740 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8397 (mt) REVERT: J 795 TYR cc_start: 0.8363 (t80) cc_final: 0.7857 (t80) REVERT: J 1261 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8279 (pp) REVERT: J 1305 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7573 (m-30) REVERT: J 1317 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6495 (pp20) REVERT: J 1361 THR cc_start: 0.8864 (m) cc_final: 0.8492 (p) REVERT: J 1368 ASP cc_start: 0.8079 (t0) cc_final: 0.7588 (m-30) REVERT: J 1370 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.5339 (mpt) REVERT: L 100 MET cc_start: 0.6427 (mtp) cc_final: 0.6190 (mpp) REVERT: L 116 GLU cc_start: 0.8564 (mp0) cc_final: 0.8356 (pm20) REVERT: L 256 PHE cc_start: 0.9195 (t80) cc_final: 0.8658 (t80) REVERT: L 429 THR cc_start: 0.8563 (m) cc_final: 0.8042 (p) REVERT: L 567 MET cc_start: 0.8931 (mtp) cc_final: 0.8546 (mtp) REVERT: L 578 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8430 (pttm) REVERT: L 589 GLN cc_start: 0.8809 (mt0) cc_final: 0.8489 (mt0) outliers start: 127 outliers final: 77 residues processed: 429 average time/residue: 0.6031 time to fit residues: 308.8104 Evaluate side-chains 430 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 335 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 327 GLN Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 620 ASN Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 954 LYS Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1136 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 663 GLU Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1236 GLU Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1317 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 571 TYR Chi-restraints excluded: chain L residue 578 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 200 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 379 optimal weight: 50.0000 chunk 102 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 335 optimal weight: 8.9990 chunk 152 optimal weight: 0.8980 chunk 346 optimal weight: 7.9990 chunk 278 optimal weight: 0.0270 chunk 172 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 343 HIS I 811 ASN L 437 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.212394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138553 restraints weight = 33423.762| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.76 r_work: 0.3289 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31749 Z= 0.122 Angle : 0.565 11.337 43214 Z= 0.296 Chirality : 0.042 0.277 4979 Planarity : 0.004 0.057 5363 Dihedral : 13.703 178.020 5241 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.15 % Rotamer: Outliers : 3.68 % Allowed : 16.64 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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: 0.11 (0.14), residues: 3755 helix: 1.61 (0.14), residues: 1519 sheet: -0.51 (0.25), residues: 421 loop : -1.14 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 388 TYR 0.042 0.001 TYR L 148 PHE 0.035 0.001 PHE L 256 TRP 0.020 0.001 TRP L 326 HIS 0.006 0.001 HIS I 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (31741) covalent geometry : angle 0.56251 / 0.30 (43202) hydrogen bonds : bond 0.03873 / 2.61 ( 1390) hydrogen bonds : angle 4.18438 / 2.87 ( 3881) metal coordination : bond 0.00499 / 0.27 ( 8) metal coordination : angle 2.92460 / 1.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 348 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 ARG cc_start: 0.7602 (ptm-80) cc_final: 0.6991 (mtt180) REVERT: G 170 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7651 (ttp-170) REVERT: H 110 VAL cc_start: 0.8867 (t) cc_final: 0.8598 (p) REVERT: H 111 THR cc_start: 0.6811 (OUTLIER) cc_final: 0.6215 (t) REVERT: H 114 ASP cc_start: 0.7000 (m-30) cc_final: 0.6662 (m-30) REVERT: I 72 SER cc_start: 0.7961 (t) cc_final: 0.7620 (m) REVERT: I 183 TRP cc_start: 0.8262 (m-10) cc_final: 0.7764 (m-10) REVERT: I 394 ARG cc_start: 0.8260 (tpp80) cc_final: 0.8033 (tpp80) REVERT: I 475 VAL cc_start: 0.6785 (p) cc_final: 0.6569 (p) REVERT: I 503 LYS cc_start: 0.7625 (tptm) cc_final: 0.6903 (ptmt) REVERT: I 516 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8073 (m-30) REVERT: I 631 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7001 (mp0) REVERT: I 672 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7942 (pm20) REVERT: I 902 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7678 (mp) REVERT: I 925 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8234 (m) REVERT: I 955 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7419 (tm-30) REVERT: I 958 LYS cc_start: 0.7686 (ttmm) cc_final: 0.7449 (ttpp) REVERT: J 66 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7206 (ptmm) REVERT: J 79 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7657 (ptpp) REVERT: J 94 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7758 (mt0) REVERT: J 129 ASP cc_start: 0.7829 (t0) cc_final: 0.7550 (t0) REVERT: J 130 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6615 (tpt) REVERT: J 158 GLN cc_start: 0.7027 (tt0) cc_final: 0.6472 (mt0) REVERT: J 219 LYS cc_start: 0.7313 (mtpp) cc_final: 0.6886 (tppp) REVERT: J 695 LYS cc_start: 0.7970 (ttpp) cc_final: 0.7610 (ttmm) REVERT: J 740 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8353 (mt) REVERT: J 795 TYR cc_start: 0.8330 (t80) cc_final: 0.7821 (t80) REVERT: J 1261 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8254 (pp) REVERT: J 1305 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7557 (m-30) REVERT: J 1317 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6567 (pp20) REVERT: J 1361 THR cc_start: 0.8833 (m) cc_final: 0.8450 (p) REVERT: J 1368 ASP cc_start: 0.8086 (t0) cc_final: 0.7590 (m-30) REVERT: J 1370 MET cc_start: 0.6871 (OUTLIER) cc_final: 0.5348 (mpt) REVERT: L 100 MET cc_start: 0.6443 (OUTLIER) cc_final: 0.6208 (mpp) REVERT: L 489 MET cc_start: 0.7882 (mtt) cc_final: 0.7423 (mtp) REVERT: L 567 MET cc_start: 0.8952 (mtp) cc_final: 0.8487 (mtp) REVERT: L 589 GLN cc_start: 0.8814 (mt0) cc_final: 0.8494 (mt0) outliers start: 117 outliers final: 75 residues processed: 421 average time/residue: 0.6160 time to fit residues: 310.1913 Evaluate side-chains 419 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 328 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 902 LEU Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 954 LYS Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 663 GLU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1236 GLU Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1317 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 362 ASN Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 507 MET Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 571 TYR Chi-restraints excluded: chain L residue 578 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 237 optimal weight: 2.9990 chunk 241 optimal weight: 5.9990 chunk 198 optimal weight: 0.8980 chunk 284 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 290 optimal weight: 40.0000 chunk 15 optimal weight: 0.1980 chunk 6 optimal weight: 0.0870 chunk 147 optimal weight: 0.5980 chunk 343 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 343 HIS I 620 ASN I 811 ASN J 777 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.211979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136266 restraints weight = 33475.117| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.73 r_work: 0.3279 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31749 Z= 0.136 Angle : 0.592 18.913 43214 Z= 0.305 Chirality : 0.042 0.287 4979 Planarity : 0.004 0.057 5363 Dihedral : 13.680 178.202 5236 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.93 % Favored : 95.05 % Rotamer: Outliers : 3.21 % Allowed : 17.26 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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: 0.13 (0.14), residues: 3755 helix: 1.60 (0.14), residues: 1520 sheet: -0.39 (0.25), residues: 413 loop : -1.13 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 388 TYR 0.045 0.001 TYR L 148 PHE 0.032 0.001 PHE L 259 TRP 0.021 0.001 TRP L 326 HIS 0.005 0.001 HIS I 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (31741) covalent geometry : angle 0.59018 / 0.30 (43202) hydrogen bonds : bond 0.03943 / 2.66 ( 1390) hydrogen bonds : angle 4.16401 / 2.85 ( 3881) metal coordination : bond 0.00575 / 0.31 ( 8) metal coordination : angle 2.79386 / 1.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 332 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 170 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7684 (ttp-170) REVERT: H 110 VAL cc_start: 0.8850 (t) cc_final: 0.8613 (p) REVERT: I 72 SER cc_start: 0.7964 (t) cc_final: 0.7622 (m) REVERT: I 183 TRP cc_start: 0.8228 (m-10) cc_final: 0.7711 (m-10) REVERT: I 394 ARG cc_start: 0.8253 (tpp80) cc_final: 0.8018 (tpp80) REVERT: I 475 VAL cc_start: 0.6725 (p) cc_final: 0.6511 (p) REVERT: I 503 LYS cc_start: 0.7605 (tptm) cc_final: 0.6847 (ptmt) REVERT: I 516 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: I 631 GLU cc_start: 0.8037 (mm-30) cc_final: 0.6988 (mp0) REVERT: I 672 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7899 (pm20) REVERT: I 866 ASP cc_start: 0.8284 (p0) cc_final: 0.7900 (p0) REVERT: I 902 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7657 (mp) REVERT: I 925 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8253 (m) REVERT: I 955 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7386 (tm-30) REVERT: I 958 LYS cc_start: 0.7647 (ttmm) cc_final: 0.7401 (ttpp) REVERT: J 66 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7207 (ptmm) REVERT: J 79 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7566 (ptpp) REVERT: J 94 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7848 (mt0) REVERT: J 130 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6642 (tpt) REVERT: J 158 GLN cc_start: 0.6985 (tt0) cc_final: 0.6433 (mt0) REVERT: J 219 LYS cc_start: 0.7287 (mtpp) cc_final: 0.6869 (tppp) REVERT: J 695 LYS cc_start: 0.7965 (ttpp) cc_final: 0.7600 (ttmm) REVERT: J 740 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8380 (mt) REVERT: J 795 TYR cc_start: 0.8331 (t80) cc_final: 0.7820 (t80) REVERT: J 1261 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8282 (pp) REVERT: J 1305 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7556 (m-30) REVERT: J 1317 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6557 (pp20) REVERT: J 1361 THR cc_start: 0.8854 (m) cc_final: 0.8475 (p) REVERT: J 1368 ASP cc_start: 0.8078 (t0) cc_final: 0.7577 (m-30) REVERT: J 1370 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.5336 (mpt) REVERT: L 100 MET cc_start: 0.6372 (OUTLIER) cc_final: 0.6142 (mpp) REVERT: L 567 MET cc_start: 0.8910 (mtp) cc_final: 0.8464 (mtp) REVERT: L 589 GLN cc_start: 0.8817 (mt0) cc_final: 0.8494 (mt0) outliers start: 102 outliers final: 73 residues processed: 398 average time/residue: 0.6126 time to fit residues: 291.0705 Evaluate side-chains 411 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 323 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 327 GLN Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 902 LEU Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 954 LYS Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 663 GLU Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1236 GLU Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1317 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 362 ASN Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 527 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 175 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 243 optimal weight: 6.9990 chunk 12 optimal weight: 0.0770 chunk 283 optimal weight: 40.0000 chunk 372 optimal weight: 10.0000 chunk 200 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 117 HIS I 343 HIS I 811 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.209787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.132605 restraints weight = 33461.158| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.72 r_work: 0.3236 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 31749 Z= 0.209 Angle : 0.644 14.927 43214 Z= 0.330 Chirality : 0.045 0.312 4979 Planarity : 0.005 0.063 5363 Dihedral : 13.766 178.470 5236 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.30 % Favored : 94.65 % Rotamer: Outliers : 3.21 % Allowed : 17.39 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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: -0.03 (0.14), residues: 3755 helix: 1.45 (0.14), residues: 1518 sheet: -0.45 (0.25), residues: 413 loop : -1.22 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 388 TYR 0.047 0.002 TYR L 148 PHE 0.027 0.002 PHE L 259 TRP 0.020 0.001 TRP L 326 HIS 0.006 0.001 HIS I1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.21 (31741) covalent geometry : angle 0.64212 / 0.33 (43202) hydrogen bonds : bond 0.04673 / 3.17 ( 1390) hydrogen bonds : angle 4.27058 / 2.93 ( 3881) metal coordination : bond 0.00960 / 0.52 ( 8) metal coordination : angle 3.04123 / 1.88 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7510 Ramachandran restraints generated. 3755 Oldfield, 0 Emsley, 3755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 329 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 170 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7777 (ttp-170) REVERT: H 110 VAL cc_start: 0.8853 (t) cc_final: 0.8577 (p) REVERT: I 72 SER cc_start: 0.7992 (t) cc_final: 0.7647 (m) REVERT: I 183 TRP cc_start: 0.8231 (m-10) cc_final: 0.7625 (m-10) REVERT: I 315 MET cc_start: 0.8551 (tpt) cc_final: 0.8312 (tpp) REVERT: I 394 ARG cc_start: 0.8249 (tpp80) cc_final: 0.7491 (tpm170) REVERT: I 475 VAL cc_start: 0.6786 (p) cc_final: 0.6565 (p) REVERT: I 503 LYS cc_start: 0.7667 (tptm) cc_final: 0.6871 (ptmt) REVERT: I 516 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: I 631 GLU cc_start: 0.7965 (mm-30) cc_final: 0.6978 (mp0) REVERT: I 672 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7865 (pm20) REVERT: I 902 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7667 (mp) REVERT: I 925 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8305 (m) REVERT: I 955 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7357 (tm-30) REVERT: I 958 LYS cc_start: 0.7683 (ttmm) cc_final: 0.7427 (ttpp) REVERT: J 66 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7307 (ptmm) REVERT: J 79 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7656 (ptpp) REVERT: J 94 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7861 (mt0) REVERT: J 130 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6643 (tpt) REVERT: J 158 GLN cc_start: 0.6977 (tt0) cc_final: 0.6371 (mt0) REVERT: J 219 LYS cc_start: 0.7340 (mtpp) cc_final: 0.6903 (tppp) REVERT: J 321 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8635 (mmmm) REVERT: J 695 LYS cc_start: 0.7960 (ttpp) cc_final: 0.7597 (ttmm) REVERT: J 740 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8459 (mt) REVERT: J 795 TYR cc_start: 0.8389 (t80) cc_final: 0.7869 (t80) REVERT: J 1305 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: J 1317 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6566 (pp20) REVERT: J 1361 THR cc_start: 0.8958 (m) cc_final: 0.8661 (p) REVERT: J 1368 ASP cc_start: 0.8066 (t0) cc_final: 0.7565 (m-30) REVERT: J 1370 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.5347 (mpt) REVERT: L 100 MET cc_start: 0.6427 (OUTLIER) cc_final: 0.6197 (mpp) REVERT: L 273 MET cc_start: 0.8431 (ppp) cc_final: 0.8167 (ppp) REVERT: L 567 MET cc_start: 0.8926 (mtp) cc_final: 0.8489 (mtp) REVERT: L 589 GLN cc_start: 0.8811 (mt0) cc_final: 0.8483 (mt0) outliers start: 102 outliers final: 73 residues processed: 397 average time/residue: 0.6456 time to fit residues: 305.0753 Evaluate side-chains 411 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 324 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 327 GLN Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 491 ASP Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 633 LEU Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 672 GLU Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 730 SER Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 854 ILE Chi-restraints excluded: chain I residue 902 LEU Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 954 LYS Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1167 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 94 GLN Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 663 GLU Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 853 THR Chi-restraints excluded: chain J residue 880 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 1236 GLU Chi-restraints excluded: chain J residue 1249 ASN Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1317 GLU Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 100 MET Chi-restraints excluded: chain L residue 362 ASN Chi-restraints excluded: chain L residue 425 TYR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 527 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 107 optimal weight: 0.8980 chunk 98 optimal weight: 0.0370 chunk 137 optimal weight: 0.0670 chunk 44 optimal weight: 2.9990 chunk 362 optimal weight: 9.9990 chunk 321 optimal weight: 50.0000 chunk 336 optimal weight: 40.0000 chunk 105 optimal weight: 1.9990 chunk 294 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 342 optimal weight: 50.0000 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 811 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.210890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136451 restraints weight = 33523.260| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.72 r_work: 0.3269 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 31749 Z= 0.152 Angle : 0.608 14.217 43214 Z= 0.312 Chirality : 0.043 0.295 4979 Planarity : 0.004 0.058 5363 Dihedral : 13.747 178.627 5236 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 2.92 % Allowed : 17.74 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.06 % 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: 0.03 (0.14), residues: 3755 helix: 1.52 (0.14), residues: 1517 sheet: -0.34 (0.26), residues: 403 loop : -1.21 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 388 TYR 0.030 0.001 TYR L 148 PHE 0.026 0.001 PHE L 259 TRP 0.020 0.001 TRP L 326 HIS 0.006 0.001 HIS I1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (31741) covalent geometry : angle 0.60561 / 0.31 (43202) hydrogen bonds : bond 0.04206 / 2.84 ( 1390) hydrogen bonds : angle 4.21062 / 2.89 ( 3881) metal coordination : bond 0.00662 / 0.36 ( 8) metal coordination : angle 3.07316 / 1.88 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14420.00 seconds wall clock time: 244 minutes 54.40 seconds (14694.40 seconds total)