Starting phenix.real_space_refine on Sat Aug 8 03:43:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t02_40931/08_2026/8t02_40931.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t02_40931/08_2026/8t02_40931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t02_40931/08_2026/8t02_40931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t02_40931/08_2026/8t02_40931.map" model { file = "/net/cci-nas-00/data/ceres_data/8t02_40931/08_2026/8t02_40931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t02_40931/08_2026/8t02_40931.cif" } resolution = 3.79 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= 0.048 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 49 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 15920 2.51 5 N 4509 2.21 5 O 5014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s 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: 25601 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1705 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 10397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1318, 10397 Classifications: {'peptide': 1318} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1262} Chain breaks: 1 Chain: "J" Number of atoms: 10240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10240 Classifications: {'peptide': 1316} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1261} Chain breaks: 3 Chain: "K" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 577 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "A" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 546 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "B" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 460 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14224 SG CYS J 70 97.450 108.353 98.961 1.00183.94 S ATOM 14238 SG CYS J 72 99.675 110.221 101.104 1.00182.54 S ATOM 14346 SG CYS J 85 98.361 112.202 98.326 1.00183.85 S ATOM 14370 SG CYS J 88 99.729 108.318 97.797 1.00184.25 S ATOM 19921 SG CYS J 814 57.298 72.229 58.546 1.00 96.28 S ATOM 20486 SG CYS J 888 60.317 72.044 60.645 1.00 85.91 S ATOM 20537 SG CYS J 895 58.588 71.307 61.359 1.00 82.58 S ATOM 20558 SG CYS J 898 58.473 70.268 61.270 1.00 84.30 S Time building chain proxies: 5.05, per 1000 atoms: 0.20 Number of scatterers: 25601 At special positions: 0 Unit cell: (166.78, 123.74, 164.628, 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 106 16.00 P 49 15.00 Mg 1 11.99 O 5014 8.00 N 4509 7.00 C 15920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 935.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " 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 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " Number of angles added : 12 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5810 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 44 sheets defined 39.3% alpha, 15.4% beta 19 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 154 through 159 removed outlier: 4.024A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE G 159 " --> pdb=" O ALA G 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 154 through 159' Processing helix chain 'G' and resid 212 through 233 removed outlier: 3.867A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 49 removed outlier: 3.660A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 removed outlier: 3.540A 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 230 removed outlier: 4.051A pdb=" N ALA H 230 " --> pdb=" O GLU H 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.502A pdb=" N LEU I 213 " --> pdb=" O ILE I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 246 Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 288 through 294 removed outlier: 3.935A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 294' Processing helix chain 'I' and resid 318 through 329 removed outlier: 4.126A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY I 329 " --> pdb=" O LEU I 325 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.790A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 391 through 393 No H-bonds generated for 'chain 'I' and resid 391 through 393' Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 437 Processing helix chain 'I' and resid 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 480 Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 539 through 543 removed outlier: 3.690A pdb=" N ALA I 543 " --> pdb=" O ARG I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 614 removed outlier: 3.887A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 609 through 614' Processing helix chain 'I' and resid 646 through 650 removed outlier: 3.958A pdb=" N VAL I 650 " --> pdb=" O ARG I 647 " (cutoff:3.500A) Processing helix chain 'I' and resid 662 through 667 removed outlier: 4.200A pdb=" N LEU I 667 " --> pdb=" O VAL I 663 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 removed outlier: 3.829A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 819 through 825 removed outlier: 4.083A pdb=" N VAL I 823 " --> pdb=" O SER I 819 " (cutoff:3.500A) Processing helix chain 'I' and resid 858 through 864 removed outlier: 3.639A pdb=" N LEU I 862 " --> pdb=" O GLY I 858 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 980 Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.627A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.909A 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: 4.431A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.725A 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: 3.567A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1138 through 1151 Processing helix chain 'I' and resid 1165 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 removed outlier: 3.592A pdb=" N TYR I1281 " --> pdb=" O ALA I1277 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1293 Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.775A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1333 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 95 through 101 removed outlier: 3.751A pdb=" N ARG J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 194 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 286 removed outlier: 4.245A 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 328 through 332 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 removed outlier: 3.521A pdb=" N ALA J 397 " --> pdb=" O THR J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 417 removed outlier: 3.889A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 458 removed outlier: 3.670A pdb=" N CYS J 454 " --> pdb=" O HIS J 450 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA J 455 " --> pdb=" O PRO J 451 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA J 456 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.823A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 593 Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.920A pdb=" N TYR J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.755A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 648 through 670 removed outlier: 4.024A pdb=" N GLU J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.810A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 4.044A pdb=" N GLN J 739 " --> pdb=" O ALA J 735 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU J 740 " --> pdb=" O GLN J 736 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.962A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY J 782 " --> pdb=" O GLY J 778 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.597A 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 896 through 900 Processing helix chain 'J' and resid 914 through 925 removed outlier: 4.307A 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 1068 through 1073 removed outlier: 3.725A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.962A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.338A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1324 removed outlier: 3.661A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1328 through 1339 Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1360 through 1373 removed outlier: 4.089A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG J1371 " --> pdb=" O GLN J1367 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG J1373 " --> pdb=" O ARG J1369 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 33 removed outlier: 4.043A pdb=" N GLY K 33 " --> pdb=" O GLN K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 62 through 74 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.958A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 53 through 61 removed outlier: 5.707A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 Processing sheet with id=AA5, first strand: chain 'H' and resid 12 through 18 removed outlier: 5.100A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.666A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.591A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.241A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE I 104 " --> pdb=" O ASP I 116 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB3, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.576A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 154 through 158 Processing sheet with id=AB5, first strand: chain 'I' and resid 180 through 181 Processing sheet with id=AB6, first strand: chain 'I' and resid 284 through 285 removed outlier: 5.229A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.753A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.939A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.562A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'I' and resid 817 through 818 removed outlier: 3.695A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA I1067 " --> pdb=" O LEU I1233 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 817 through 818 removed outlier: 3.695A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.676A pdb=" N THR I 843 " --> pdb=" O GLY I 846 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 882 through 884 removed outlier: 7.137A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 887 through 888 Processing sheet with id=AD1, first strand: chain 'I' and resid 1244 through 1245 removed outlier: 3.502A pdb=" N GLN J 435 " --> pdb=" O LEU J 423 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 1244 through 1245 removed outlier: 7.119A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU J 449 " --> pdb=" O VAL J 354 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR J 356 " --> pdb=" O LEU J 449 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AD4, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AD5, first strand: chain 'J' and resid 34 through 37 removed outlier: 5.239A pdb=" N SER J 34 " --> pdb=" O MET J 102 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N HIS J 104 " --> pdb=" O SER J 34 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY J 36 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU J 106 " --> pdb=" O GLY J 36 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 159 through 160 removed outlier: 3.539A pdb=" N VAL J 145 " --> pdb=" O LYS J 179 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS J 179 " --> pdb=" O VAL J 145 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE J 147 " --> pdb=" O ASP J 177 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 526 through 527 removed outlier: 3.641A pdb=" N ILE J 552 " --> pdb=" O SER J 568 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER J 568 " --> pdb=" O ILE J 552 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AD9, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE1, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'J' and resid 991 through 996 removed outlier: 3.873A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU J 984 " --> pdb=" O GLU J 993 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL J1011 " --> pdb=" O GLY J 956 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AE4, first strand: chain 'J' and resid 1001 through 1002 Processing sheet with id=AE5, first strand: chain 'J' and resid 1098 through 1100 removed outlier: 4.530A pdb=" N VAL J1113 " --> pdb=" O VAL J1035 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1046 through 1049 removed outlier: 3.825A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1188 through 1190 removed outlier: 3.725A pdb=" N VAL J1204 " --> pdb=" O GLY J1161 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.541A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1020 hydrogen bonds defined for protein. 2841 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 5.78 Time building geometry restraints manager: 2.48 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: 8504 1.34 - 1.46: 3819 1.46 - 1.58: 13479 1.58 - 1.70: 95 1.70 - 1.82: 184 Bond restraints: 26081 Sorted by residual: bond pdb=" C1' DT B 105 " pdb=" N1 DT B 105 " ideal model delta sigma weight residual 1.468 1.527 -0.059 1.40e-02 5.10e+03 1.77e+01 bond pdb=" C1' DT B 122 " pdb=" N1 DT B 122 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.37e+01 bond pdb=" C1' DT B 121 " pdb=" N1 DT B 121 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.34e+01 bond pdb=" C1' DT B 103 " pdb=" N1 DT B 103 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.18e+01 bond pdb=" C3' DA A 13 " pdb=" O3' DA A 13 " ideal model delta sigma weight residual 1.435 1.478 -0.043 1.30e-02 5.92e+03 1.08e+01 ... (remaining 26076 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 34719 1.95 - 3.89: 639 3.89 - 5.84: 65 5.84 - 7.78: 7 7.78 - 9.73: 2 Bond angle restraints: 35432 Sorted by residual: angle pdb=" N3 DT B 108 " pdb=" C4 DT B 108 " pdb=" O4 DT B 108 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT B 114 " pdb=" C4 DT B 114 " pdb=" O4 DT B 114 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT B 121 " pdb=" C4 DT B 121 " pdb=" O4 DT B 121 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT B 106 " pdb=" C4 DT B 106 " pdb=" O4 DT B 106 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT B 107 " pdb=" C4 DT B 107 " pdb=" O4 DT B 107 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 35427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.02: 15339 34.02 - 68.04: 597 68.04 - 102.06: 32 102.06 - 136.08: 0 136.08 - 170.10: 3 Dihedral angle restraints: 15971 sinusoidal: 6941 harmonic: 9030 Sorted by residual: dihedral pdb=" CA ASP J1184 " pdb=" C ASP J1184 " pdb=" N PRO J1185 " pdb=" CA PRO J1185 " ideal model delta harmonic sigma weight residual -180.00 -149.31 -30.69 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA ASN I 519 " pdb=" C ASN I 519 " pdb=" N PRO I 520 " pdb=" CA PRO I 520 " ideal model delta harmonic sigma weight residual 180.00 150.82 29.18 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA SER J 753 " pdb=" C SER J 753 " pdb=" N ILE J 754 " pdb=" CA ILE J 754 " ideal model delta harmonic sigma weight residual -180.00 -153.63 -26.37 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 15968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2835 0.037 - 0.073: 792 0.073 - 0.110: 276 0.110 - 0.146: 131 0.146 - 0.183: 17 Chirality restraints: 4051 Sorted by residual: chirality pdb=" C3' DA A 11 " pdb=" C4' DA A 11 " pdb=" O3' DA A 11 " pdb=" C2' DA A 11 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.33e-01 chirality pdb=" C3' DA A 14 " pdb=" C4' DA A 14 " pdb=" O3' DA A 14 " pdb=" C2' DA A 14 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" C3' DA A 18 " pdb=" C4' DA A 18 " pdb=" O3' DA A 18 " pdb=" C2' DA A 18 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.17 2.00e-01 2.50e+01 6.82e-01 ... (remaining 4048 not shown) Planarity restraints: 4467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY J 358 " -0.046 5.00e-02 4.00e+02 7.00e-02 7.84e+00 pdb=" N PRO J 359 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO J 359 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO J 359 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS I 697 " -0.042 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO I 698 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO I 698 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO I 698 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 850 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO J 851 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO J 851 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 851 " 0.033 5.00e-02 4.00e+02 ... (remaining 4464 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 324 2.56 - 3.15: 22503 3.15 - 3.73: 40195 3.73 - 4.32: 53892 4.32 - 4.90: 88714 Nonbonded interactions: 205628 Sorted by model distance: nonbonded pdb=" OE1 GLU I 562 " pdb=" OG SER I 662 " model vdw 1.981 3.040 nonbonded pdb=" OG1 THR G 22 " pdb=" O THR G 207 " model vdw 1.991 3.040 nonbonded pdb=" OG SER I 421 " pdb=" OD1 ASP I 423 " model vdw 2.014 3.040 nonbonded pdb=" OG1 THR I 6 " pdb=" OD2 ASP I 781 " model vdw 2.018 3.040 nonbonded pdb=" OH TYR J 360 " pdb=" OE1 GLN J 448 " model vdw 2.052 3.040 ... (remaining 205623 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 7 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 149 or (resid 150 and (name N or \ name CA or name C or name O or name CB )) or resid 151 through 158 or resid 170 \ through 232)) selection = (chain 'H' and (resid 7 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.720 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26089 Z= 0.216 Angle : 0.899 83.021 35444 Z= 0.393 Chirality : 0.044 0.183 4051 Planarity : 0.004 0.070 4467 Dihedral : 16.694 170.103 10161 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.52 % Favored : 92.45 % Rotamer: Outliers : 1.53 % Allowed : 16.25 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.15), residues: 3124 helix: 0.80 (0.16), residues: 1065 sheet: -1.28 (0.25), residues: 362 loop : -1.67 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I1033 TYR 0.024 0.001 TYR I1229 PHE 0.017 0.001 PHE I 230 TRP 0.011 0.001 TRP J 236 HIS 0.005 0.001 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.21 (26081) covalent geometry : angle 0.62899 / 0.38 (35432) hydrogen bonds : bond 0.15933 / 10.75 ( 1046) hydrogen bonds : angle 6.49414 / 4.58 ( 2917) metal coordination : bond 0.04809 / 2.39 ( 8) metal coordination : angle 34.94997 / 18.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 746 time to evaluate : 0.965 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: 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: 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 10 LYS cc_start: 0.8160 (mmtm) cc_final: 0.7319 (mppt) REVERT: G 58 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6611 (mt-10) REVERT: G 199 ASP cc_start: 0.7504 (m-30) cc_final: 0.7125 (m-30) REVERT: H 128 HIS cc_start: 0.8333 (t-90) cc_final: 0.7668 (t-90) REVERT: I 14 ASP cc_start: 0.8078 (t0) cc_final: 0.7801 (t0) REVERT: I 37 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8007 (tptt) REVERT: I 211 ARG cc_start: 0.8428 (ttt180) cc_final: 0.8153 (ptt180) REVERT: I 218 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8615 (pp20) REVERT: I 359 ARG cc_start: 0.7577 (ttt-90) cc_final: 0.6759 (ttt-90) REVERT: I 360 LEU cc_start: 0.8841 (tt) cc_final: 0.8638 (tt) REVERT: I 361 SER cc_start: 0.9110 (m) cc_final: 0.8875 (p) REVERT: I 731 ARG cc_start: 0.7986 (ptp90) cc_final: 0.7715 (ptp90) REVERT: I 1089 GLU cc_start: 0.8014 (tp30) cc_final: 0.7606 (tp30) REVERT: I 1090 ASN cc_start: 0.8692 (t0) cc_final: 0.8438 (t0) REVERT: I 1240 ASP cc_start: 0.8568 (p0) cc_final: 0.7987 (t0) REVERT: I 1281 TYR cc_start: 0.8339 (m-80) cc_final: 0.7861 (m-10) REVERT: J 425 ARG cc_start: 0.7336 (ttt180) cc_final: 0.6801 (mtp-110) REVERT: J 462 ASP cc_start: 0.8178 (p0) cc_final: 0.7743 (p0) REVERT: J 553 THR cc_start: 0.8763 (m) cc_final: 0.8305 (p) REVERT: J 568 SER cc_start: 0.8329 (m) cc_final: 0.7563 (m) REVERT: J 569 LEU cc_start: 0.8794 (tp) cc_final: 0.8437 (tp) REVERT: J 614 LEU cc_start: 0.8876 (tp) cc_final: 0.8518 (tt) REVERT: J 1040 MET cc_start: 0.3368 (mtt) cc_final: 0.0603 (ppp) REVERT: J 1280 VAL cc_start: 0.6943 (m) cc_final: 0.6143 (m) REVERT: K 61 ASN cc_start: 0.8216 (m-40) cc_final: 0.7825 (t0) outliers start: 41 outliers final: 25 residues processed: 769 average time/residue: 0.1941 time to fit residues: 225.5204 Evaluate side-chains 561 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 536 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 1042 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain J residue 341 ASN Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 833 GLU Chi-restraints excluded: chain J residue 1116 SER Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1334 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 0.0870 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 75 GLN G 186 ASN I 120 GLN I 133 ASN ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 339 ASN I 490 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 952 GLN I1146 GLN I1220 GLN J 157 GLN J 465 GLN J 488 ASN J 865 HIS J1010 GLN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS K 7 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.207622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.140722 restraints weight = 44705.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141657 restraints weight = 27623.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143071 restraints weight = 16909.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.143743 restraints weight = 15455.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.143895 restraints weight = 14046.896| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26089 Z= 0.167 Angle : 0.801 36.566 35444 Z= 0.385 Chirality : 0.046 0.270 4051 Planarity : 0.006 0.084 4467 Dihedral : 14.571 176.417 4068 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.11 % Favored : 93.85 % Rotamer: Outliers : 3.25 % Allowed : 19.16 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.15), residues: 3124 helix: 0.75 (0.16), residues: 1096 sheet: -1.13 (0.24), residues: 400 loop : -1.67 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 403 TYR 0.017 0.002 TYR J 772 PHE 0.019 0.002 PHE I 80 TRP 0.020 0.002 TRP I 997 HIS 0.006 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (26081) covalent geometry : angle 0.74166 / 0.38 (35432) hydrogen bonds : bond 0.05038 / 3.45 ( 1046) hydrogen bonds : angle 5.52034 / 3.91 ( 2917) metal coordination : bond 0.01738 / 0.77 ( 8) metal coordination : angle 16.49327 / 8.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 592 time to evaluate : 0.898 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: 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 58 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7072 (mt-10) REVERT: G 125 LYS cc_start: 0.8599 (tttt) cc_final: 0.8120 (tttm) REVERT: G 199 ASP cc_start: 0.7568 (m-30) cc_final: 0.6864 (m-30) REVERT: H 147 GLN cc_start: 0.8305 (tm-30) cc_final: 0.8012 (tm-30) REVERT: H 200 LYS cc_start: 0.8160 (tttp) cc_final: 0.7686 (tptt) REVERT: I 8 LYS cc_start: 0.9023 (mttt) cc_final: 0.8542 (mttm) REVERT: I 37 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8067 (tptt) REVERT: I 97 ARG cc_start: 0.7600 (mmm-85) cc_final: 0.7199 (mmm-85) REVERT: I 121 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8243 (tm-30) REVERT: I 130 MET cc_start: 0.8268 (ttm) cc_final: 0.7955 (ttm) REVERT: I 211 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8305 (ptt180) REVERT: I 369 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8237 (tmm) REVERT: I 384 LEU cc_start: 0.8679 (tt) cc_final: 0.8408 (mt) REVERT: I 653 MET cc_start: 0.8042 (tpp) cc_final: 0.7751 (tpt) REVERT: I 731 ARG cc_start: 0.7845 (ptp90) cc_final: 0.7564 (ptp90) REVERT: I 737 ASN cc_start: 0.8852 (t0) cc_final: 0.8645 (t0) REVERT: I 932 GLN cc_start: 0.6221 (tp40) cc_final: 0.5874 (tp40) REVERT: I 933 VAL cc_start: 0.7881 (t) cc_final: 0.7124 (t) REVERT: I 958 LYS cc_start: 0.9125 (tmtt) cc_final: 0.8664 (tptp) REVERT: I 1072 ASN cc_start: 0.8462 (p0) cc_final: 0.8172 (p0) REVERT: I 1089 GLU cc_start: 0.8107 (tp30) cc_final: 0.7762 (tp30) REVERT: I 1090 ASN cc_start: 0.8694 (t0) cc_final: 0.8474 (t0) REVERT: I 1166 ASP cc_start: 0.8553 (m-30) cc_final: 0.7886 (t0) REVERT: I 1170 MET cc_start: 0.8121 (mmt) cc_final: 0.7781 (mmt) REVERT: I 1174 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8147 (tp30) REVERT: I 1229 TYR cc_start: 0.8326 (m-10) cc_final: 0.8106 (m-10) REVERT: I 1281 TYR cc_start: 0.8645 (m-80) cc_final: 0.8346 (m-10) REVERT: J 417 ARG cc_start: 0.8209 (tpt170) cc_final: 0.7545 (mmm160) REVERT: J 425 ARG cc_start: 0.7334 (ttt180) cc_final: 0.6832 (mtp-110) REVERT: J 449 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7396 (tp) REVERT: J 462 ASP cc_start: 0.8300 (p0) cc_final: 0.7925 (p0) REVERT: J 739 GLN cc_start: 0.8319 (pt0) cc_final: 0.8026 (pt0) REVERT: J 891 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7406 (t0) REVERT: J 1003 LEU cc_start: 0.8036 (tp) cc_final: 0.7783 (tp) REVERT: J 1040 MET cc_start: 0.3708 (mtt) cc_final: 0.0649 (ppp) REVERT: J 1189 MET cc_start: 0.7504 (ttm) cc_final: 0.7083 (tmm) REVERT: J 1224 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7805 (tpp80) REVERT: K 48 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8456 (t) REVERT: K 61 ASN cc_start: 0.8416 (m-40) cc_final: 0.8025 (t0) outliers start: 87 outliers final: 39 residues processed: 640 average time/residue: 0.1836 time to fit residues: 180.1681 Evaluate side-chains 543 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 498 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1119 ASP Chi-restraints excluded: chain J residue 1224 ARG Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1314 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 178 optimal weight: 20.0000 chunk 139 optimal weight: 50.0000 chunk 62 optimal weight: 6.9990 chunk 278 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 198 optimal weight: 30.0000 chunk 110 optimal weight: 4.9990 chunk 286 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 117 optimal weight: 0.0170 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 75 GLN G 186 ASN ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN ** J 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.202407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.130971 restraints weight = 44674.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132591 restraints weight = 28813.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.132675 restraints weight = 18174.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.133140 restraints weight = 17663.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.133477 restraints weight = 16106.027| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 26089 Z= 0.312 Angle : 0.827 27.758 35444 Z= 0.411 Chirality : 0.048 0.231 4051 Planarity : 0.006 0.081 4467 Dihedral : 14.652 179.061 4042 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.20 % Favored : 92.77 % Rotamer: Outliers : 4.41 % Allowed : 19.80 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 1.57 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.14), residues: 3124 helix: 0.48 (0.15), residues: 1109 sheet: -1.06 (0.25), residues: 405 loop : -1.75 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG K 67 TYR 0.029 0.002 TYR J 795 PHE 0.018 0.002 PHE J 35 TRP 0.015 0.002 TRP I 997 HIS 0.007 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00714 / 0.31 (26081) covalent geometry : angle 0.79481 / 0.41 (35432) hydrogen bonds : bond 0.04960 / 3.39 ( 1046) hydrogen bonds : angle 5.56404 / 3.95 ( 2917) metal coordination : bond 0.01856 / 0.81 ( 8) metal coordination : angle 12.49665 / 6.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 496 time to evaluate : 1.125 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: 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: symmetry clash REVERT: G 125 LYS cc_start: 0.8604 (tttt) cc_final: 0.8044 (tttm) REVERT: G 186 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8372 (p0) REVERT: H 18 GLN cc_start: 0.8929 (pm20) cc_final: 0.8556 (mp10) REVERT: H 152 TYR cc_start: 0.7422 (t80) cc_final: 0.7221 (t80) REVERT: H 215 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8032 (tm-30) REVERT: I 8 LYS cc_start: 0.9175 (mttt) cc_final: 0.8608 (mttm) REVERT: I 37 LYS cc_start: 0.8619 (ttpt) cc_final: 0.8115 (tptt) REVERT: I 97 ARG cc_start: 0.7713 (mmm-85) cc_final: 0.7102 (mmm-85) REVERT: I 121 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8297 (tm-30) REVERT: I 130 MET cc_start: 0.8541 (ttm) cc_final: 0.8263 (ttm) REVERT: I 133 ASN cc_start: 0.8177 (t160) cc_final: 0.7936 (t0) REVERT: I 202 ARG cc_start: 0.8481 (ptt180) cc_final: 0.8090 (ptt180) REVERT: I 211 ARG cc_start: 0.8814 (ttt180) cc_final: 0.8413 (ptt180) REVERT: I 448 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7965 (mt) REVERT: I 477 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8874 (mt-10) REVERT: I 731 ARG cc_start: 0.8089 (ptp90) cc_final: 0.7606 (ptp90) REVERT: I 820 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7485 (tp30) REVERT: I 932 GLN cc_start: 0.6151 (tp40) cc_final: 0.5800 (tp40) REVERT: I 958 LYS cc_start: 0.9272 (tmtt) cc_final: 0.8745 (tptp) REVERT: I 1089 GLU cc_start: 0.8229 (tp30) cc_final: 0.7894 (tp30) REVERT: I 1166 ASP cc_start: 0.8758 (m-30) cc_final: 0.7839 (t0) REVERT: I 1170 MET cc_start: 0.8450 (mmt) cc_final: 0.8005 (mmt) REVERT: I 1174 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8012 (tp30) REVERT: I 1194 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: I 1230 MET cc_start: 0.8690 (ttp) cc_final: 0.8299 (ttt) REVERT: I 1240 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8040 (t0) REVERT: I 1246 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8009 (ttm-80) REVERT: I 1281 TYR cc_start: 0.8892 (m-80) cc_final: 0.8469 (m-10) REVERT: I 1304 MET cc_start: 0.7755 (ttm) cc_final: 0.7422 (ttm) REVERT: J 37 GLU cc_start: 0.7816 (tp30) cc_final: 0.7615 (tp30) REVERT: J 102 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7546 (tpp) REVERT: J 192 MET cc_start: 0.6339 (mmm) cc_final: 0.6051 (mmm) REVERT: J 417 ARG cc_start: 0.8337 (tpt170) cc_final: 0.7821 (mmm160) REVERT: J 449 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8040 (mt) REVERT: J 475 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8519 (mm-30) REVERT: J 569 LEU cc_start: 0.9052 (tp) cc_final: 0.8842 (tp) REVERT: J 835 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7482 (tp) REVERT: J 891 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7708 (t0) REVERT: J 1003 LEU cc_start: 0.7975 (tp) cc_final: 0.7649 (tp) REVERT: J 1040 MET cc_start: 0.4307 (mtt) cc_final: 0.1401 (ppp) REVERT: J 1156 LEU cc_start: 0.9724 (OUTLIER) cc_final: 0.9475 (tp) REVERT: J 1189 MET cc_start: 0.7845 (ttm) cc_final: 0.7323 (tmm) REVERT: J 1281 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7803 (tm-30) REVERT: K 44 ASP cc_start: 0.8048 (p0) cc_final: 0.7445 (p0) REVERT: K 48 VAL cc_start: 0.8970 (OUTLIER) cc_final: 0.8729 (t) REVERT: K 52 ARG cc_start: 0.8832 (mtp180) cc_final: 0.8290 (ptm160) REVERT: K 61 ASN cc_start: 0.8679 (m-40) cc_final: 0.8240 (t0) outliers start: 118 outliers final: 74 residues processed: 575 average time/residue: 0.1793 time to fit residues: 158.9225 Evaluate side-chains 550 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 463 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 224 PHE Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 425 ILE Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 477 GLU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 613 ASN Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 763 THR Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 820 GLU Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 959 ASP Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1246 ARG Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 568 SER Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 867 GLN Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1156 LEU Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 161 optimal weight: 0.8980 chunk 221 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 75 GLN ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1090 ASN J 720 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.206071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.132487 restraints weight = 44201.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137171 restraints weight = 23821.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137900 restraints weight = 17341.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.139523 restraints weight = 14120.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.139788 restraints weight = 12630.594| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26089 Z= 0.157 Angle : 0.717 16.379 35444 Z= 0.357 Chirality : 0.044 0.230 4051 Planarity : 0.005 0.066 4467 Dihedral : 14.633 177.398 4040 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.08 % Favored : 93.89 % Rotamer: Outliers : 3.74 % Allowed : 21.33 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.14), residues: 3124 helix: 0.64 (0.16), residues: 1097 sheet: -0.97 (0.25), residues: 391 loop : -1.63 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 540 TYR 0.037 0.001 TYR H 177 PHE 0.014 0.001 PHE J1319 TRP 0.011 0.001 TRP I1276 HIS 0.010 0.001 HIS I1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (26081) covalent geometry : angle 0.70203 / 0.36 (35432) hydrogen bonds : bond 0.04382 / 2.98 ( 1046) hydrogen bonds : angle 5.26928 / 3.75 ( 2917) metal coordination : bond 0.01132 / 0.50 ( 8) metal coordination : angle 7.95306 / 4.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 521 time to evaluate : 0.968 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.6991 (mmtm) REVERT: G 75 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7911 (pp30) REVERT: G 199 ASP cc_start: 0.7133 (m-30) cc_final: 0.6774 (m-30) REVERT: G 206 GLU cc_start: 0.6979 (tp30) cc_final: 0.6594 (tp30) REVERT: H 18 GLN cc_start: 0.8898 (pm20) cc_final: 0.8535 (mp10) REVERT: I 37 LYS cc_start: 0.8570 (ttpt) cc_final: 0.8076 (tptt) REVERT: I 97 ARG cc_start: 0.7644 (mmm-85) cc_final: 0.6982 (mmm-85) REVERT: I 121 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8318 (tm-30) REVERT: I 130 MET cc_start: 0.8420 (ttm) cc_final: 0.8138 (ttm) REVERT: I 133 ASN cc_start: 0.8233 (t160) cc_final: 0.7974 (t0) REVERT: I 151 ARG cc_start: 0.8118 (ttt-90) cc_final: 0.7810 (mtp85) REVERT: I 202 ARG cc_start: 0.8382 (ptt180) cc_final: 0.8166 (ptt180) REVERT: I 211 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8253 (ptt180) REVERT: I 369 MET cc_start: 0.8302 (tmm) cc_final: 0.7993 (tmm) REVERT: I 431 LYS cc_start: 0.8680 (tppt) cc_final: 0.8426 (tppt) REVERT: I 565 GLU cc_start: 0.8034 (mp0) cc_final: 0.7832 (mp0) REVERT: I 575 LEU cc_start: 0.8796 (tp) cc_final: 0.8178 (mt) REVERT: I 731 ARG cc_start: 0.7975 (ptp90) cc_final: 0.7472 (ptp90) REVERT: I 932 GLN cc_start: 0.6426 (tp40) cc_final: 0.6053 (tp40) REVERT: I 933 VAL cc_start: 0.8070 (t) cc_final: 0.7530 (t) REVERT: I 951 MET cc_start: 0.9025 (tmm) cc_final: 0.8677 (ppp) REVERT: I 958 LYS cc_start: 0.9281 (tmtt) cc_final: 0.8832 (tptp) REVERT: I 1089 GLU cc_start: 0.8189 (tp30) cc_final: 0.7812 (tp30) REVERT: I 1166 ASP cc_start: 0.8508 (m-30) cc_final: 0.7743 (t0) REVERT: I 1170 MET cc_start: 0.8193 (mmt) cc_final: 0.7802 (mmt) REVERT: I 1174 GLU cc_start: 0.8619 (mm-30) cc_final: 0.7972 (tp30) REVERT: I 1194 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: I 1230 MET cc_start: 0.8656 (ttp) cc_final: 0.8335 (ttt) REVERT: I 1246 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.7997 (ttm-80) REVERT: I 1281 TYR cc_start: 0.8811 (m-80) cc_final: 0.8495 (m-10) REVERT: I 1290 MET cc_start: 0.8458 (tpp) cc_final: 0.7765 (tpp) REVERT: J 102 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7551 (tpp) REVERT: J 180 MET cc_start: 0.7455 (tpt) cc_final: 0.7252 (tpp) REVERT: J 192 MET cc_start: 0.6327 (mmm) cc_final: 0.5998 (mmm) REVERT: J 298 MET cc_start: 0.5753 (mmt) cc_final: 0.5435 (tmm) REVERT: J 339 ARG cc_start: 0.7222 (mmm-85) cc_final: 0.6870 (mmm-85) REVERT: J 340 GLN cc_start: 0.7636 (tp40) cc_final: 0.7366 (tp40) REVERT: J 417 ARG cc_start: 0.8187 (tpt170) cc_final: 0.7709 (mmm160) REVERT: J 449 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7914 (mt) REVERT: J 462 ASP cc_start: 0.8240 (p0) cc_final: 0.8000 (p0) REVERT: J 569 LEU cc_start: 0.9037 (tp) cc_final: 0.8816 (tp) REVERT: J 646 ILE cc_start: 0.8465 (mm) cc_final: 0.7767 (tp) REVERT: J 709 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8194 (ptt-90) REVERT: J 821 MET cc_start: 0.8216 (tpp) cc_final: 0.7474 (tpp) REVERT: J 835 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7346 (tp) REVERT: J 891 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7423 (t0) REVERT: J 1003 LEU cc_start: 0.7848 (tp) cc_final: 0.7462 (tp) REVERT: J 1040 MET cc_start: 0.4354 (mtt) cc_final: 0.1462 (ppp) REVERT: J 1156 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9443 (tp) REVERT: J 1189 MET cc_start: 0.7808 (ttm) cc_final: 0.7282 (tmm) REVERT: J 1297 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8377 (pttp) REVERT: K 12 LYS cc_start: 0.9487 (ttmt) cc_final: 0.9278 (ttmt) REVERT: K 26 ARG cc_start: 0.8591 (tpm170) cc_final: 0.7858 (tpm170) REVERT: K 48 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8532 (t) REVERT: K 52 ARG cc_start: 0.8925 (mtp180) cc_final: 0.8286 (ptm160) REVERT: K 61 ASN cc_start: 0.8639 (m-40) cc_final: 0.8193 (t0) outliers start: 100 outliers final: 68 residues processed: 579 average time/residue: 0.1836 time to fit residues: 165.0686 Evaluate side-chains 555 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 474 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 224 PHE Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 757 THR Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1246 ARG Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 330 MET Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 817 HIS Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 867 GLN Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1156 LEU Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1297 LYS Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 92 optimal weight: 0.8980 chunk 271 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 27 optimal weight: 30.0000 chunk 3 optimal weight: 5.9990 chunk 232 optimal weight: 0.9980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 684 ASN I1090 ASN J 274 ASN ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 720 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.205637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.138504 restraints weight = 44287.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.138451 restraints weight = 28713.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.138052 restraints weight = 20945.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.138592 restraints weight = 18732.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.139222 restraints weight = 16646.134| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26089 Z= 0.173 Angle : 0.703 14.322 35444 Z= 0.354 Chirality : 0.045 0.421 4051 Planarity : 0.005 0.090 4467 Dihedral : 14.615 175.552 4036 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.08 % Favored : 93.89 % Rotamer: Outliers : 4.37 % Allowed : 21.67 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.15), residues: 3124 helix: 0.68 (0.16), residues: 1095 sheet: -0.93 (0.25), residues: 392 loop : -1.60 (0.14), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J1148 TYR 0.063 0.002 TYR H 177 PHE 0.018 0.001 PHE J1319 TRP 0.010 0.001 TRP J 580 HIS 0.009 0.001 HIS H 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (26081) covalent geometry : angle 0.69474 / 0.35 (35432) hydrogen bonds : bond 0.04248 / 2.89 ( 1046) hydrogen bonds : angle 5.19167 / 3.69 ( 2917) metal coordination : bond 0.00957 / 0.43 ( 8) metal coordination : angle 5.82011 / 2.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 501 time to evaluate : 0.954 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: 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 10 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.6969 (mmtm) REVERT: G 33 ARG cc_start: 0.8471 (mmm160) cc_final: 0.8251 (tpp80) REVERT: G 71 LYS cc_start: 0.8461 (tptt) cc_final: 0.8104 (tptm) REVERT: H 132 HIS cc_start: 0.7541 (m-70) cc_final: 0.7293 (m-70) REVERT: I 37 LYS cc_start: 0.8588 (ttpt) cc_final: 0.8099 (tptt) REVERT: I 97 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.6898 (mmm-85) REVERT: I 121 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8345 (tm-30) REVERT: I 130 MET cc_start: 0.8418 (ttm) cc_final: 0.8143 (ttm) REVERT: I 133 ASN cc_start: 0.8284 (t160) cc_final: 0.7937 (t0) REVERT: I 202 ARG cc_start: 0.8371 (ptt180) cc_final: 0.8131 (ptt180) REVERT: I 211 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8247 (ptt180) REVERT: I 369 MET cc_start: 0.8392 (tmm) cc_final: 0.8187 (tmm) REVERT: I 431 LYS cc_start: 0.8739 (tppt) cc_final: 0.8480 (tppt) REVERT: I 731 ARG cc_start: 0.7960 (ptp90) cc_final: 0.7514 (ptp90) REVERT: I 820 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7415 (tp30) REVERT: I 932 GLN cc_start: 0.6531 (tp40) cc_final: 0.6119 (tp40) REVERT: I 933 VAL cc_start: 0.7997 (t) cc_final: 0.7400 (t) REVERT: I 958 LYS cc_start: 0.9281 (tmtt) cc_final: 0.8837 (tptp) REVERT: I 1023 HIS cc_start: 0.8926 (m90) cc_final: 0.8722 (m90) REVERT: I 1089 GLU cc_start: 0.8209 (tp30) cc_final: 0.7836 (tp30) REVERT: I 1166 ASP cc_start: 0.8859 (m-30) cc_final: 0.7932 (t0) REVERT: I 1170 MET cc_start: 0.8360 (mmt) cc_final: 0.7928 (mmt) REVERT: I 1174 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8011 (tp30) REVERT: I 1194 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: I 1230 MET cc_start: 0.8752 (ttp) cc_final: 0.8443 (ttt) REVERT: I 1240 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.7926 (t70) REVERT: I 1246 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7988 (ttm-80) REVERT: I 1281 TYR cc_start: 0.8869 (m-80) cc_final: 0.8559 (m-10) REVERT: I 1290 MET cc_start: 0.8349 (tpp) cc_final: 0.7667 (tpp) REVERT: J 180 MET cc_start: 0.7449 (tpt) cc_final: 0.7091 (tpp) REVERT: J 192 MET cc_start: 0.6365 (mmm) cc_final: 0.5997 (mmm) REVERT: J 237 MET cc_start: 0.6776 (mpp) cc_final: 0.6411 (mpp) REVERT: J 298 MET cc_start: 0.5639 (mmt) cc_final: 0.5299 (tmm) REVERT: J 342 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6976 (mt) REVERT: J 417 ARG cc_start: 0.8169 (tpt170) cc_final: 0.7686 (mmm160) REVERT: J 449 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7499 (tp) REVERT: J 569 LEU cc_start: 0.9049 (tp) cc_final: 0.8841 (tp) REVERT: J 835 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7365 (tt) REVERT: J 844 THR cc_start: 0.8337 (p) cc_final: 0.8067 (t) REVERT: J 1003 LEU cc_start: 0.7844 (tp) cc_final: 0.7488 (tp) REVERT: J 1040 MET cc_start: 0.4332 (mtt) cc_final: 0.1528 (ppp) REVERT: J 1156 LEU cc_start: 0.9665 (OUTLIER) cc_final: 0.9428 (tp) REVERT: J 1189 MET cc_start: 0.7800 (ttm) cc_final: 0.7292 (tmm) REVERT: J 1297 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8218 (pttp) REVERT: K 12 LYS cc_start: 0.9545 (ttmt) cc_final: 0.9247 (ttmt) REVERT: K 30 MET cc_start: 0.8154 (ptm) cc_final: 0.7758 (mtt) REVERT: K 44 ASP cc_start: 0.7962 (p0) cc_final: 0.7464 (p0) REVERT: K 48 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8642 (t) REVERT: K 52 ARG cc_start: 0.8941 (mtp180) cc_final: 0.8158 (ptm160) REVERT: K 61 ASN cc_start: 0.8620 (m-40) cc_final: 0.8171 (t0) outliers start: 117 outliers final: 80 residues processed: 570 average time/residue: 0.1862 time to fit residues: 165.0506 Evaluate side-chains 563 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 471 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 191 ARG Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 224 PHE Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 757 THR Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 820 GLU Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1246 ARG Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 568 SER Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 817 HIS Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1156 LEU Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1297 LYS Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 166 optimal weight: 0.0970 chunk 299 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 245 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN I1090 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.207439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.143112 restraints weight = 44365.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.142122 restraints weight = 25376.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.143065 restraints weight = 17548.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.143928 restraints weight = 16067.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.144069 restraints weight = 14491.951| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26089 Z= 0.137 Angle : 0.686 14.829 35444 Z= 0.345 Chirality : 0.044 0.251 4051 Planarity : 0.005 0.066 4467 Dihedral : 14.585 174.228 4036 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 4.15 % Allowed : 22.53 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.15), residues: 3124 helix: 0.72 (0.16), residues: 1093 sheet: -0.85 (0.25), residues: 402 loop : -1.56 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J1148 TYR 0.033 0.001 TYR H 177 PHE 0.020 0.001 PHE J1319 TRP 0.018 0.001 TRP I1276 HIS 0.004 0.001 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (26081) covalent geometry : angle 0.68145 / 0.34 (35432) hydrogen bonds : bond 0.04059 / 2.74 ( 1046) hydrogen bonds : angle 5.03853 / 3.60 ( 2917) metal coordination : bond 0.00640 / 0.30 ( 8) metal coordination : angle 4.30034 / 2.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 520 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7181 (mmtm) REVERT: G 71 LYS cc_start: 0.8463 (tptt) cc_final: 0.8128 (tptm) REVERT: G 125 LYS cc_start: 0.8547 (tttt) cc_final: 0.7980 (tttm) REVERT: G 145 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8082 (tptp) REVERT: G 199 ASP cc_start: 0.7076 (m-30) cc_final: 0.6694 (m-30) REVERT: H 51 MET cc_start: 0.8502 (tpp) cc_final: 0.8206 (tpp) REVERT: H 132 HIS cc_start: 0.7602 (m-70) cc_final: 0.7360 (m-70) REVERT: H 147 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8586 (tm-30) REVERT: I 37 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8064 (tptt) REVERT: I 97 ARG cc_start: 0.7652 (mmm-85) cc_final: 0.7169 (mmm-85) REVERT: I 121 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8406 (tm-30) REVERT: I 133 ASN cc_start: 0.8264 (t160) cc_final: 0.8024 (t0) REVERT: I 202 ARG cc_start: 0.8366 (ptt180) cc_final: 0.8148 (ptt180) REVERT: I 211 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8303 (ptt180) REVERT: I 369 MET cc_start: 0.8416 (tmm) cc_final: 0.7901 (tmm) REVERT: I 431 LYS cc_start: 0.8665 (tppt) cc_final: 0.8369 (tppt) REVERT: I 575 LEU cc_start: 0.8628 (tp) cc_final: 0.8082 (mt) REVERT: I 653 MET cc_start: 0.7889 (tpp) cc_final: 0.7084 (tpt) REVERT: I 731 ARG cc_start: 0.8009 (ptp90) cc_final: 0.7488 (ptp90) REVERT: I 932 GLN cc_start: 0.6426 (tp40) cc_final: 0.5972 (tp40) REVERT: I 933 VAL cc_start: 0.7965 (t) cc_final: 0.7433 (t) REVERT: I 951 MET cc_start: 0.8949 (tmm) cc_final: 0.8635 (ppp) REVERT: I 958 LYS cc_start: 0.9237 (tmtt) cc_final: 0.8673 (tptp) REVERT: I 1023 HIS cc_start: 0.8867 (m90) cc_final: 0.8609 (m90) REVERT: I 1089 GLU cc_start: 0.8132 (tp30) cc_final: 0.7707 (tp30) REVERT: I 1166 ASP cc_start: 0.8755 (m-30) cc_final: 0.7856 (t0) REVERT: I 1170 MET cc_start: 0.8216 (mmt) cc_final: 0.7854 (mmt) REVERT: I 1174 GLU cc_start: 0.8601 (mm-30) cc_final: 0.7946 (tp30) REVERT: I 1194 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7910 (mt-10) REVERT: I 1230 MET cc_start: 0.8730 (ttp) cc_final: 0.8418 (ttt) REVERT: I 1240 ASP cc_start: 0.8558 (p0) cc_final: 0.7766 (t70) REVERT: I 1241 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8405 (t0) REVERT: I 1246 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.7935 (ttm-80) REVERT: I 1281 TYR cc_start: 0.8807 (m-80) cc_final: 0.8506 (m-10) REVERT: I 1332 SER cc_start: 0.7380 (OUTLIER) cc_final: 0.7091 (p) REVERT: J 42 GLU cc_start: 0.8577 (mp0) cc_final: 0.8185 (tt0) REVERT: J 180 MET cc_start: 0.7449 (tpt) cc_final: 0.7009 (tpp) REVERT: J 192 MET cc_start: 0.6433 (mmm) cc_final: 0.6024 (mmm) REVERT: J 237 MET cc_start: 0.6751 (mpp) cc_final: 0.6477 (mpp) REVERT: J 417 ARG cc_start: 0.8073 (tpt170) cc_final: 0.7440 (mmm160) REVERT: J 449 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7618 (tp) REVERT: J 604 MET cc_start: 0.8215 (ttt) cc_final: 0.7934 (ttt) REVERT: J 835 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7345 (tt) REVERT: J 844 THR cc_start: 0.8270 (p) cc_final: 0.8028 (t) REVERT: J 891 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7417 (t0) REVERT: J 1003 LEU cc_start: 0.7858 (tp) cc_final: 0.7537 (tp) REVERT: J 1040 MET cc_start: 0.4567 (mtt) cc_final: 0.1620 (ppp) REVERT: J 1155 ILE cc_start: 0.9417 (mm) cc_final: 0.9194 (tp) REVERT: J 1156 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9414 (tp) REVERT: J 1189 MET cc_start: 0.7672 (ttm) cc_final: 0.7083 (tmm) REVERT: J 1297 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8038 (pttp) REVERT: K 12 LYS cc_start: 0.9549 (ttmt) cc_final: 0.9244 (ttmt) REVERT: K 44 ASP cc_start: 0.8048 (p0) cc_final: 0.7532 (p0) REVERT: K 48 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8512 (t) REVERT: K 52 ARG cc_start: 0.8958 (mtp180) cc_final: 0.8170 (ptm160) REVERT: K 61 ASN cc_start: 0.8539 (m-40) cc_final: 0.8154 (t0) outliers start: 111 outliers final: 72 residues processed: 594 average time/residue: 0.1841 time to fit residues: 170.5735 Evaluate side-chains 561 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 478 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 191 ARG Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 224 PHE Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 757 THR Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 865 LEU Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1246 ARG Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 568 SER Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 694 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 817 HIS Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1156 LEU Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1297 LYS Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 210 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 296 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 315 optimal weight: 50.0000 chunk 73 optimal weight: 20.0000 chunk 267 optimal weight: 20.0000 chunk 8 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 GLN I 133 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN I1090 ASN J 430 HIS ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 739 GLN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.202560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.128641 restraints weight = 44426.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.132387 restraints weight = 25885.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133569 restraints weight = 16059.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.133676 restraints weight = 16211.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.133885 restraints weight = 15190.203| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 26089 Z= 0.277 Angle : 0.766 13.080 35444 Z= 0.388 Chirality : 0.046 0.277 4051 Planarity : 0.006 0.075 4467 Dihedral : 14.632 173.285 4035 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.56 % Favored : 93.37 % Rotamer: Outliers : 4.89 % Allowed : 22.15 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 1.57 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 3124 helix: 0.58 (0.16), residues: 1113 sheet: -0.89 (0.25), residues: 418 loop : -1.59 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 339 TYR 0.029 0.002 TYR J 772 PHE 0.024 0.002 PHE J1319 TRP 0.027 0.002 TRP I1276 HIS 0.007 0.001 HIS I 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.28 (26081) covalent geometry : angle 0.76190 / 0.39 (35432) hydrogen bonds : bond 0.04488 / 3.06 ( 1046) hydrogen bonds : angle 5.21802 / 3.71 ( 2917) metal coordination : bond 0.01281 / 0.58 ( 8) metal coordination : angle 4.44288 / 2.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 481 time to evaluate : 1.008 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: 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 10 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7225 (mmtm) REVERT: G 32 GLU cc_start: 0.6979 (mp0) cc_final: 0.6770 (mp0) REVERT: G 33 ARG cc_start: 0.7707 (tpp80) cc_final: 0.7378 (mmt-90) REVERT: G 71 LYS cc_start: 0.8474 (tptt) cc_final: 0.8232 (tptm) REVERT: G 125 LYS cc_start: 0.8538 (tttt) cc_final: 0.8001 (tttm) REVERT: G 199 ASP cc_start: 0.7355 (m-30) cc_final: 0.6812 (m-30) REVERT: H 18 GLN cc_start: 0.8767 (pm20) cc_final: 0.8257 (mp10) REVERT: H 147 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8751 (tm-30) REVERT: H 200 LYS cc_start: 0.8155 (tttp) cc_final: 0.7841 (tptt) REVERT: I 37 LYS cc_start: 0.8625 (ttpt) cc_final: 0.8138 (tptt) REVERT: I 97 ARG cc_start: 0.7699 (mmm-85) cc_final: 0.7337 (mmt90) REVERT: I 121 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8378 (tm-30) REVERT: I 202 ARG cc_start: 0.8409 (ptt180) cc_final: 0.8164 (ptt180) REVERT: I 211 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8400 (ptt180) REVERT: I 369 MET cc_start: 0.8398 (tmm) cc_final: 0.7984 (tmm) REVERT: I 431 LYS cc_start: 0.8734 (tppt) cc_final: 0.8485 (tppt) REVERT: I 432 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8767 (tt) REVERT: I 731 ARG cc_start: 0.8182 (ptp90) cc_final: 0.7633 (ptp90) REVERT: I 820 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7541 (tp30) REVERT: I 951 MET cc_start: 0.9017 (tmm) cc_final: 0.8647 (ppp) REVERT: I 958 LYS cc_start: 0.9301 (tmtt) cc_final: 0.8827 (tptp) REVERT: I 1023 HIS cc_start: 0.8938 (m90) cc_final: 0.8701 (m90) REVERT: I 1034 ARG cc_start: 0.9444 (tpt90) cc_final: 0.9009 (tpt90) REVERT: I 1089 GLU cc_start: 0.8292 (tp30) cc_final: 0.7908 (tp30) REVERT: I 1166 ASP cc_start: 0.8801 (m-30) cc_final: 0.7932 (t0) REVERT: I 1170 MET cc_start: 0.8307 (mmt) cc_final: 0.7957 (mmt) REVERT: I 1174 GLU cc_start: 0.8691 (mm-30) cc_final: 0.7957 (tp30) REVERT: I 1194 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7924 (mt-10) REVERT: I 1230 MET cc_start: 0.8811 (ttp) cc_final: 0.8470 (ttt) REVERT: I 1240 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8067 (t70) REVERT: I 1246 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8122 (ttm-80) REVERT: I 1281 TYR cc_start: 0.8977 (m-80) cc_final: 0.8550 (m-10) REVERT: I 1332 SER cc_start: 0.7248 (OUTLIER) cc_final: 0.6997 (p) REVERT: J 123 ARG cc_start: 0.7635 (mmm160) cc_final: 0.6960 (mmp80) REVERT: J 180 MET cc_start: 0.7426 (tpt) cc_final: 0.7036 (tpp) REVERT: J 192 MET cc_start: 0.6616 (mmm) cc_final: 0.6143 (mmm) REVERT: J 237 MET cc_start: 0.6861 (mpp) cc_final: 0.6595 (mpp) REVERT: J 341 ASN cc_start: 0.8669 (m110) cc_final: 0.7213 (t0) REVERT: J 342 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7301 (mm) REVERT: J 417 ARG cc_start: 0.8193 (tpt170) cc_final: 0.7589 (mmm160) REVERT: J 449 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7977 (mt) REVERT: J 821 MET cc_start: 0.8560 (mmm) cc_final: 0.7645 (tpp) REVERT: J 835 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7322 (tt) REVERT: J 844 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8153 (t) REVERT: J 891 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7734 (t0) REVERT: J 1003 LEU cc_start: 0.7925 (tp) cc_final: 0.7610 (tp) REVERT: J 1040 MET cc_start: 0.4377 (mtt) cc_final: 0.1591 (ppp) REVERT: J 1156 LEU cc_start: 0.9669 (tp) cc_final: 0.9422 (tp) REVERT: J 1189 MET cc_start: 0.7908 (ttm) cc_final: 0.7370 (tmm) REVERT: K 12 LYS cc_start: 0.9551 (ttmt) cc_final: 0.9288 (ttmt) REVERT: K 44 ASP cc_start: 0.8188 (p0) cc_final: 0.7689 (p0) REVERT: K 48 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8518 (t) REVERT: K 52 ARG cc_start: 0.8928 (mtp180) cc_final: 0.8085 (ptm160) REVERT: K 61 ASN cc_start: 0.8636 (m-40) cc_final: 0.8165 (t0) REVERT: K 70 GLN cc_start: 0.9332 (tm-30) cc_final: 0.8688 (pp30) outliers start: 131 outliers final: 98 residues processed: 564 average time/residue: 0.1865 time to fit residues: 162.8779 Evaluate side-chains 562 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 450 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 191 ARG Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 425 ILE Chi-restraints excluded: chain I residue 432 LEU Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 757 THR Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 820 GLU Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 865 LEU Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1246 ARG Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 694 SER Chi-restraints excluded: chain J residue 709 ARG Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 817 HIS Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 867 GLN Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 892 PHE Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1220 ILE Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 249 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 chunk 195 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 272 optimal weight: 30.0000 chunk 171 optimal weight: 7.9990 chunk 180 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 243 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.205576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.134392 restraints weight = 44373.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.139040 restraints weight = 24037.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.138973 restraints weight = 15479.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.139400 restraints weight = 15101.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.139601 restraints weight = 14307.238| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26089 Z= 0.165 Angle : 0.721 14.336 35444 Z= 0.362 Chirality : 0.045 0.336 4051 Planarity : 0.005 0.088 4467 Dihedral : 14.596 173.160 4035 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 4.18 % Allowed : 24.43 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.15), residues: 3124 helix: 0.64 (0.16), residues: 1107 sheet: -0.81 (0.25), residues: 425 loop : -1.54 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I1033 TYR 0.021 0.002 TYR I1285 PHE 0.025 0.002 PHE J1319 TRP 0.021 0.002 TRP I1276 HIS 0.005 0.001 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (26081) covalent geometry : angle 0.71845 / 0.36 (35432) hydrogen bonds : bond 0.04185 / 2.83 ( 1046) hydrogen bonds : angle 5.09508 / 3.64 ( 2917) metal coordination : bond 0.00663 / 0.30 ( 8) metal coordination : angle 3.43986 / 1.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 488 time to evaluate : 0.781 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: 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: symmetry clash REVERT: G 10 LYS cc_start: 0.8222 (mmtm) cc_final: 0.7276 (mmtm) REVERT: G 32 GLU cc_start: 0.6873 (mp0) cc_final: 0.6547 (mp0) REVERT: G 33 ARG cc_start: 0.7526 (tpp80) cc_final: 0.7138 (mmt-90) REVERT: G 58 GLU cc_start: 0.7777 (tt0) cc_final: 0.7408 (tt0) REVERT: G 71 LYS cc_start: 0.8506 (tptt) cc_final: 0.8208 (tptm) REVERT: G 125 LYS cc_start: 0.8538 (tttt) cc_final: 0.7942 (tttm) REVERT: G 199 ASP cc_start: 0.7409 (m-30) cc_final: 0.6725 (m-30) REVERT: H 18 GLN cc_start: 0.8715 (pm20) cc_final: 0.8404 (mp10) REVERT: H 132 HIS cc_start: 0.7635 (m-70) cc_final: 0.7334 (m-70) REVERT: H 147 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8779 (tm-30) REVERT: H 200 LYS cc_start: 0.8059 (tttp) cc_final: 0.7793 (tptt) REVERT: H 204 GLU cc_start: 0.8700 (tt0) cc_final: 0.8164 (tp30) REVERT: I 37 LYS cc_start: 0.8634 (ttpt) cc_final: 0.8120 (tptt) REVERT: I 97 ARG cc_start: 0.7538 (mmm-85) cc_final: 0.7241 (mmm-85) REVERT: I 121 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8480 (tm-30) REVERT: I 151 ARG cc_start: 0.8065 (ttt-90) cc_final: 0.7844 (ttt-90) REVERT: I 169 LYS cc_start: 0.8102 (tttt) cc_final: 0.7620 (pttp) REVERT: I 202 ARG cc_start: 0.8356 (ptt180) cc_final: 0.8104 (ptt180) REVERT: I 211 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8361 (ptt180) REVERT: I 369 MET cc_start: 0.8382 (tmm) cc_final: 0.7993 (tmm) REVERT: I 431 LYS cc_start: 0.8704 (tppt) cc_final: 0.8397 (tppt) REVERT: I 540 ARG cc_start: 0.8372 (ttm110) cc_final: 0.7958 (ttm110) REVERT: I 575 LEU cc_start: 0.8773 (tp) cc_final: 0.8177 (mt) REVERT: I 731 ARG cc_start: 0.8069 (ptp90) cc_final: 0.7596 (ptp90) REVERT: I 932 GLN cc_start: 0.6457 (tp40) cc_final: 0.5984 (tp40) REVERT: I 951 MET cc_start: 0.9042 (tmm) cc_final: 0.8668 (ppp) REVERT: I 958 LYS cc_start: 0.9277 (tmtt) cc_final: 0.8815 (tptp) REVERT: I 1023 HIS cc_start: 0.8965 (m90) cc_final: 0.8750 (m90) REVERT: I 1089 GLU cc_start: 0.8196 (tp30) cc_final: 0.7772 (tp30) REVERT: I 1166 ASP cc_start: 0.8758 (m-30) cc_final: 0.7802 (t0) REVERT: I 1170 MET cc_start: 0.8270 (mmt) cc_final: 0.7893 (mmt) REVERT: I 1174 GLU cc_start: 0.8658 (mm-30) cc_final: 0.7975 (tp30) REVERT: I 1194 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: I 1230 MET cc_start: 0.8758 (ttp) cc_final: 0.8387 (ttt) REVERT: I 1240 ASP cc_start: 0.8552 (p0) cc_final: 0.7869 (t70) REVERT: I 1241 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8530 (t0) REVERT: I 1246 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7852 (ttm-80) REVERT: I 1281 TYR cc_start: 0.8860 (m-80) cc_final: 0.8469 (m-10) REVERT: I 1332 SER cc_start: 0.7282 (OUTLIER) cc_final: 0.6981 (p) REVERT: J 123 ARG cc_start: 0.7594 (mmm160) cc_final: 0.6927 (mmp80) REVERT: J 192 MET cc_start: 0.6494 (mmm) cc_final: 0.6018 (mmm) REVERT: J 341 ASN cc_start: 0.8555 (m110) cc_final: 0.7125 (t0) REVERT: J 342 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7168 (mt) REVERT: J 417 ARG cc_start: 0.8040 (tpt170) cc_final: 0.7446 (mmm160) REVERT: J 449 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7379 (tp) REVERT: J 568 SER cc_start: 0.8901 (t) cc_final: 0.8359 (m) REVERT: J 646 ILE cc_start: 0.8517 (mm) cc_final: 0.8199 (mm) REVERT: J 821 MET cc_start: 0.8507 (mmm) cc_final: 0.7669 (tpp) REVERT: J 835 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7409 (tt) REVERT: J 844 THR cc_start: 0.8353 (p) cc_final: 0.8091 (t) REVERT: J 891 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7373 (t0) REVERT: J 1003 LEU cc_start: 0.7974 (tp) cc_final: 0.7663 (tp) REVERT: J 1040 MET cc_start: 0.4378 (mtt) cc_final: 0.1684 (ppp) REVERT: J 1156 LEU cc_start: 0.9639 (tp) cc_final: 0.9422 (tp) REVERT: J 1189 MET cc_start: 0.7859 (ttm) cc_final: 0.7241 (tmm) REVERT: K 12 LYS cc_start: 0.9548 (ttmt) cc_final: 0.9296 (ttmt) REVERT: K 44 ASP cc_start: 0.8053 (p0) cc_final: 0.7775 (p0) REVERT: K 51 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.8017 (mp) REVERT: K 52 ARG cc_start: 0.8950 (mtp180) cc_final: 0.8117 (ptm160) REVERT: K 61 ASN cc_start: 0.8611 (m-40) cc_final: 0.8275 (t0) outliers start: 112 outliers final: 86 residues processed: 564 average time/residue: 0.1651 time to fit residues: 145.4528 Evaluate side-chains 569 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 473 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 191 ARG Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 224 PHE Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 757 THR Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 865 LEU Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1246 ARG Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 694 SER Chi-restraints excluded: chain J residue 703 THR 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 803 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 817 HIS Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 51 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 250 optimal weight: 0.6980 chunk 284 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 246 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 270 optimal weight: 0.0050 chunk 50 optimal weight: 0.7980 chunk 298 optimal weight: 9.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.207385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141608 restraints weight = 44552.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.141406 restraints weight = 27723.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.140944 restraints weight = 20210.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.141620 restraints weight = 18663.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.143341 restraints weight = 16269.101| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26089 Z= 0.142 Angle : 0.724 18.644 35444 Z= 0.360 Chirality : 0.044 0.314 4051 Planarity : 0.005 0.063 4467 Dihedral : 14.533 172.506 4035 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.73 % Favored : 94.24 % Rotamer: Outliers : 3.47 % Allowed : 24.65 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.15), residues: 3124 helix: 0.64 (0.16), residues: 1107 sheet: -0.74 (0.25), residues: 415 loop : -1.51 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I1033 TYR 0.018 0.001 TYR I 726 PHE 0.035 0.002 PHE I 80 TRP 0.021 0.002 TRP I1276 HIS 0.005 0.001 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (26081) covalent geometry : angle 0.72270 / 0.36 (35432) hydrogen bonds : bond 0.04054 / 2.75 ( 1046) hydrogen bonds : angle 4.97362 / 3.55 ( 2917) metal coordination : bond 0.00476 / 0.22 ( 8) metal coordination : angle 2.77663 / 1.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 505 time to evaluate : 0.843 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: 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 10 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7244 (mmtm) REVERT: G 32 GLU cc_start: 0.6824 (mp0) cc_final: 0.6509 (mp0) REVERT: G 33 ARG cc_start: 0.7634 (tpp80) cc_final: 0.7286 (mmt-90) REVERT: G 58 GLU cc_start: 0.7718 (tt0) cc_final: 0.7326 (tt0) REVERT: G 71 LYS cc_start: 0.8497 (tptt) cc_final: 0.8252 (tptm) REVERT: G 125 LYS cc_start: 0.8540 (tttt) cc_final: 0.7949 (tttm) REVERT: G 145 LYS cc_start: 0.8534 (tptp) cc_final: 0.6913 (tptp) REVERT: G 199 ASP cc_start: 0.7364 (m-30) cc_final: 0.6683 (m-30) REVERT: H 18 GLN cc_start: 0.8697 (pm20) cc_final: 0.8401 (mp10) REVERT: H 132 HIS cc_start: 0.7618 (m-70) cc_final: 0.7311 (m-70) REVERT: H 147 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8738 (tm-30) REVERT: H 200 LYS cc_start: 0.8015 (tttp) cc_final: 0.7786 (tptt) REVERT: I 37 LYS cc_start: 0.8576 (ttpt) cc_final: 0.7913 (tptm) REVERT: I 97 ARG cc_start: 0.7616 (mmm-85) cc_final: 0.7196 (mmm-85) REVERT: I 121 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8532 (tm-30) REVERT: I 130 MET cc_start: 0.8507 (ttm) cc_final: 0.8305 (ttm) REVERT: I 151 ARG cc_start: 0.8095 (ttt-90) cc_final: 0.7842 (ttt-90) REVERT: I 169 LYS cc_start: 0.8181 (tttt) cc_final: 0.7730 (pttp) REVERT: I 202 ARG cc_start: 0.8399 (ptt180) cc_final: 0.8163 (ptt180) REVERT: I 211 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8370 (ptt180) REVERT: I 369 MET cc_start: 0.8359 (tmm) cc_final: 0.8064 (tmm) REVERT: I 431 LYS cc_start: 0.8665 (tppt) cc_final: 0.8364 (tppt) REVERT: I 540 ARG cc_start: 0.8357 (ttm110) cc_final: 0.7946 (ttm110) REVERT: I 575 LEU cc_start: 0.8779 (tp) cc_final: 0.8153 (mt) REVERT: I 731 ARG cc_start: 0.8086 (ptp90) cc_final: 0.7596 (ptp90) REVERT: I 865 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.7643 (mt) REVERT: I 932 GLN cc_start: 0.6418 (tp40) cc_final: 0.5948 (tp40) REVERT: I 958 LYS cc_start: 0.9246 (tmtt) cc_final: 0.8728 (tptp) REVERT: I 1023 HIS cc_start: 0.8905 (m90) cc_final: 0.8672 (m90) REVERT: I 1034 ARG cc_start: 0.9423 (tpt90) cc_final: 0.9043 (tpt90) REVERT: I 1089 GLU cc_start: 0.8162 (tp30) cc_final: 0.7708 (tp30) REVERT: I 1166 ASP cc_start: 0.8699 (m-30) cc_final: 0.7760 (t0) REVERT: I 1170 MET cc_start: 0.8271 (mmt) cc_final: 0.7899 (mmt) REVERT: I 1174 GLU cc_start: 0.8591 (mm-30) cc_final: 0.7960 (tp30) REVERT: I 1194 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: I 1230 MET cc_start: 0.8762 (ttp) cc_final: 0.8371 (ttt) REVERT: I 1240 ASP cc_start: 0.8579 (p0) cc_final: 0.7842 (t70) REVERT: I 1241 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8546 (t0) REVERT: I 1246 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7909 (ttm-80) REVERT: I 1281 TYR cc_start: 0.8829 (m-80) cc_final: 0.8541 (m-10) REVERT: I 1332 SER cc_start: 0.7007 (OUTLIER) cc_final: 0.6717 (p) REVERT: J 123 ARG cc_start: 0.7616 (mmm160) cc_final: 0.6997 (mmp80) REVERT: J 180 MET cc_start: 0.7474 (tpt) cc_final: 0.6954 (tpp) REVERT: J 192 MET cc_start: 0.6498 (mmm) cc_final: 0.6009 (mmm) REVERT: J 237 MET cc_start: 0.6831 (mpp) cc_final: 0.6459 (mpp) REVERT: J 417 ARG cc_start: 0.8112 (tpt170) cc_final: 0.7769 (mmm160) REVERT: J 449 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7614 (tp) REVERT: J 568 SER cc_start: 0.8845 (t) cc_final: 0.8309 (m) REVERT: J 821 MET cc_start: 0.8478 (mmm) cc_final: 0.8205 (tpp) REVERT: J 835 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7409 (tt) REVERT: J 844 THR cc_start: 0.8281 (p) cc_final: 0.8039 (t) REVERT: J 891 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7365 (t0) REVERT: J 1003 LEU cc_start: 0.7993 (tp) cc_final: 0.7699 (tp) REVERT: J 1040 MET cc_start: 0.4718 (mtt) cc_final: 0.1817 (ppp) REVERT: J 1156 LEU cc_start: 0.9608 (tp) cc_final: 0.9403 (tp) REVERT: J 1189 MET cc_start: 0.7826 (ttm) cc_final: 0.7226 (tmm) REVERT: J 1281 GLU cc_start: 0.7699 (tm-30) cc_final: 0.6823 (tp30) REVERT: K 12 LYS cc_start: 0.9548 (ttmt) cc_final: 0.9299 (ttmt) REVERT: K 29 GLN cc_start: 0.9062 (mt0) cc_final: 0.8089 (tm-30) REVERT: K 30 MET cc_start: 0.7568 (mmt) cc_final: 0.6839 (mmt) REVERT: K 61 ASN cc_start: 0.8597 (m-40) cc_final: 0.8155 (t0) outliers start: 93 outliers final: 74 residues processed: 569 average time/residue: 0.1643 time to fit residues: 145.6138 Evaluate side-chains 565 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 481 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 191 ARG Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 865 LEU Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1246 ARG Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 694 SER Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 817 HIS Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 25 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 73 optimal weight: 20.0000 chunk 173 optimal weight: 6.9990 chunk 238 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 284 optimal weight: 9.9990 chunk 161 optimal weight: 0.5980 chunk 33 optimal weight: 0.0970 chunk 230 optimal weight: 0.9990 chunk 297 optimal weight: 7.9990 chunk 220 optimal weight: 0.0070 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 GLN I 46 GLN I 339 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.207320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134061 restraints weight = 44591.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.139325 restraints weight = 22501.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141955 restraints weight = 15135.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.143310 restraints weight = 12176.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.143796 restraints weight = 10942.795| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26089 Z= 0.148 Angle : 0.735 14.439 35444 Z= 0.366 Chirality : 0.045 0.315 4051 Planarity : 0.005 0.064 4467 Dihedral : 14.512 172.054 4033 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 3.18 % Allowed : 25.14 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.15), residues: 3124 helix: 0.63 (0.16), residues: 1107 sheet: -0.64 (0.26), residues: 405 loop : -1.50 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I1033 TYR 0.017 0.001 TYR I 726 PHE 0.047 0.002 PHE I 337 TRP 0.023 0.002 TRP I1276 HIS 0.004 0.001 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (26081) covalent geometry : angle 0.73418 / 0.37 (35432) hydrogen bonds : bond 0.03989 / 2.70 ( 1046) hydrogen bonds : angle 4.97428 / 3.56 ( 2917) metal coordination : bond 0.00516 / 0.24 ( 8) metal coordination : angle 2.48444 / 1.21 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 493 time to evaluate : 0.699 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: 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 10 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7193 (mmtm) REVERT: G 32 GLU cc_start: 0.6688 (mp0) cc_final: 0.6473 (mp0) REVERT: G 58 GLU cc_start: 0.7684 (tt0) cc_final: 0.7375 (tt0) REVERT: G 71 LYS cc_start: 0.8486 (tptt) cc_final: 0.8261 (tptm) REVERT: G 97 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8004 (tm-30) REVERT: G 125 LYS cc_start: 0.8515 (tttt) cc_final: 0.7971 (tttm) REVERT: G 145 LYS cc_start: 0.8277 (tptp) cc_final: 0.7771 (tptp) REVERT: G 199 ASP cc_start: 0.7257 (m-30) cc_final: 0.6671 (m-30) REVERT: H 18 GLN cc_start: 0.8625 (pm20) cc_final: 0.8358 (mp10) REVERT: H 132 HIS cc_start: 0.7562 (m-70) cc_final: 0.7234 (m-70) REVERT: H 147 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8572 (tm-30) REVERT: H 200 LYS cc_start: 0.7980 (tttp) cc_final: 0.7673 (tptt) REVERT: H 208 ASN cc_start: 0.9295 (p0) cc_final: 0.9027 (p0) REVERT: I 37 LYS cc_start: 0.8525 (ttpt) cc_final: 0.7810 (tttm) REVERT: I 97 ARG cc_start: 0.7459 (mmm-85) cc_final: 0.7112 (mmm-85) REVERT: I 121 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8411 (tm-30) REVERT: I 130 MET cc_start: 0.8546 (ttm) cc_final: 0.8322 (ttm) REVERT: I 151 ARG cc_start: 0.8132 (ttt-90) cc_final: 0.7855 (ttt-90) REVERT: I 202 ARG cc_start: 0.8415 (ptt180) cc_final: 0.8188 (ptt180) REVERT: I 211 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8221 (ptt180) REVERT: I 369 MET cc_start: 0.8276 (tmm) cc_final: 0.7933 (tmm) REVERT: I 431 LYS cc_start: 0.8702 (tppt) cc_final: 0.8416 (tppt) REVERT: I 575 LEU cc_start: 0.8726 (tp) cc_final: 0.8139 (mt) REVERT: I 731 ARG cc_start: 0.8061 (ptp90) cc_final: 0.7511 (ptp90) REVERT: I 865 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.7630 (mt) REVERT: I 932 GLN cc_start: 0.6411 (tp40) cc_final: 0.5993 (tp40) REVERT: I 958 LYS cc_start: 0.9249 (tmtt) cc_final: 0.8749 (tptp) REVERT: I 1023 HIS cc_start: 0.8930 (m90) cc_final: 0.8699 (m90) REVERT: I 1034 ARG cc_start: 0.9398 (tpt90) cc_final: 0.9044 (tpt90) REVERT: I 1089 GLU cc_start: 0.8200 (tp30) cc_final: 0.7741 (tp30) REVERT: I 1166 ASP cc_start: 0.8204 (m-30) cc_final: 0.7578 (t0) REVERT: I 1170 MET cc_start: 0.7886 (mmt) cc_final: 0.7667 (mmt) REVERT: I 1174 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7894 (tp30) REVERT: I 1194 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: I 1230 MET cc_start: 0.8727 (ttp) cc_final: 0.8297 (ttt) REVERT: I 1240 ASP cc_start: 0.8501 (p0) cc_final: 0.7796 (t70) REVERT: I 1241 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8485 (t0) REVERT: I 1246 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7912 (ttm-80) REVERT: I 1281 TYR cc_start: 0.8827 (m-80) cc_final: 0.8551 (m-10) REVERT: I 1332 SER cc_start: 0.6958 (OUTLIER) cc_final: 0.6750 (p) REVERT: J 123 ARG cc_start: 0.7608 (mmm160) cc_final: 0.7007 (mmp80) REVERT: J 180 MET cc_start: 0.7361 (tpt) cc_final: 0.6981 (tpp) REVERT: J 189 LEU cc_start: 0.9393 (mp) cc_final: 0.8992 (pp) REVERT: J 192 MET cc_start: 0.6516 (mmm) cc_final: 0.6054 (mmm) REVERT: J 237 MET cc_start: 0.6828 (mpp) cc_final: 0.6528 (mpp) REVERT: J 341 ASN cc_start: 0.8590 (m110) cc_final: 0.7008 (t0) REVERT: J 404 GLU cc_start: 0.7749 (tp30) cc_final: 0.7321 (tp30) REVERT: J 417 ARG cc_start: 0.8036 (tpt170) cc_final: 0.7516 (mmm160) REVERT: J 449 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7628 (tp) REVERT: J 490 ILE cc_start: 0.9328 (pt) cc_final: 0.8891 (mt) REVERT: J 568 SER cc_start: 0.8816 (t) cc_final: 0.8315 (m) REVERT: J 604 MET cc_start: 0.7879 (ttt) cc_final: 0.7576 (ttt) REVERT: J 646 ILE cc_start: 0.8136 (mm) cc_final: 0.7409 (tp) REVERT: J 835 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7516 (tt) REVERT: J 844 THR cc_start: 0.8247 (p) cc_final: 0.8031 (t) REVERT: J 891 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7334 (t0) REVERT: J 1003 LEU cc_start: 0.8005 (tp) cc_final: 0.7716 (tp) REVERT: J 1040 MET cc_start: 0.4927 (mtt) cc_final: 0.1995 (ppp) REVERT: J 1156 LEU cc_start: 0.9594 (tp) cc_final: 0.9383 (tp) REVERT: J 1189 MET cc_start: 0.7658 (ttm) cc_final: 0.7072 (tmm) REVERT: J 1281 GLU cc_start: 0.7721 (tm-30) cc_final: 0.6823 (tp30) REVERT: K 29 GLN cc_start: 0.8660 (mt0) cc_final: 0.8000 (tm-30) REVERT: K 30 MET cc_start: 0.6988 (mmt) cc_final: 0.6536 (mmt) REVERT: K 61 ASN cc_start: 0.8427 (m-40) cc_final: 0.8042 (t0) outliers start: 85 outliers final: 71 residues processed: 551 average time/residue: 0.1621 time to fit residues: 138.6777 Evaluate side-chains 566 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 485 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 191 ARG Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 727 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 865 LEU Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1246 ARG Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 694 SER Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 817 HIS Chi-restraints excluded: chain J residue 835 LEU Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 25 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 166 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 190 optimal weight: 50.0000 chunk 140 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 209 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.205766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.133116 restraints weight = 44337.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.137804 restraints weight = 25247.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.139772 restraints weight = 15474.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.139909 restraints weight = 13605.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.140208 restraints weight = 13714.865| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26089 Z= 0.182 Angle : 0.746 14.551 35444 Z= 0.372 Chirality : 0.045 0.301 4051 Planarity : 0.006 0.092 4467 Dihedral : 14.528 171.821 4033 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.02 % Favored : 93.95 % Rotamer: Outliers : 3.36 % Allowed : 25.33 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.15), residues: 3124 helix: 0.63 (0.16), residues: 1110 sheet: -0.80 (0.25), residues: 426 loop : -1.46 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG J 388 TYR 0.023 0.001 TYR J 772 PHE 0.036 0.002 PHE I 337 TRP 0.026 0.002 TRP I1276 HIS 0.005 0.001 HIS J1366 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (26081) covalent geometry : angle 0.74453 / 0.37 (35432) hydrogen bonds : bond 0.04048 / 2.75 ( 1046) hydrogen bonds : angle 4.98748 / 3.55 ( 2917) metal coordination : bond 0.00736 / 0.33 ( 8) metal coordination : angle 2.55743 / 1.27 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5031.56 seconds wall clock time: 87 minutes 30.83 seconds (5250.83 seconds total)