Starting phenix.real_space_refine on Sun Sep 13 23:27:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mko_23901/09_2026/7mko_23901.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mko_23901/09_2026/7mko_23901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mko_23901/09_2026/7mko_23901.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mko_23901/09_2026/7mko_23901.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mko_23901/09_2026/7mko_23901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mko_23901/09_2026/7mko_23901.map" model { file = "/net/cci-nas-00/data/ceres_data/7mko_23901/09_2026/7mko_23901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mko_23901/09_2026/7mko_23901.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 63 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16253 2.51 5 N 4652 2.21 5 O 5192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.30s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26269 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1794 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain: "B" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "C" Number of atoms: 10414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1320, 10414 Classifications: {'peptide': 1320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1264} Chain breaks: 1 Chain: "D" Number of atoms: 10419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1344, 10419 Classifications: {'peptide': 1344} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 55, 'TRANS': 1288} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 546 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "N" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "R" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 244 Classifications: {'RNAv2': 11} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 583 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {' MG': 1, ' ZN': 2, '2TM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14459 SG CYS D 70 18.688 104.023 76.170 1.00 78.71 S ATOM 14473 SG CYS D 72 18.980 106.965 73.987 1.00 79.04 S ATOM 14581 SG CYS D 85 16.360 104.678 73.284 1.00 73.63 S ATOM 14605 SG CYS D 88 19.900 103.740 72.560 1.00 74.07 S ATOM 20293 SG CYS D 814 33.429 37.780 77.850 1.00 41.29 S ATOM 20858 SG CYS D 888 35.339 41.067 77.440 1.00 38.47 S ATOM 20909 SG CYS D 895 34.295 39.745 80.540 1.00 34.69 S ATOM 20930 SG CYS D 898 36.728 38.164 79.128 1.00 35.95 S Time building chain proxies: 5.65, per 1000 atoms: 0.22 Number of scatterers: 26269 At special positions: 0 Unit cell: (125.4, 158.4, 163.68, 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 63 15.00 Mg 1 11.99 O 5192 8.00 N 4652 7.00 C 16253 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 72 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 85 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 88 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 70 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 895 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 898 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 814 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 888 " Number of angles added : 12 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5896 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 40 sheets defined 39.4% alpha, 17.3% beta 22 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 4.03 Creating SS restraints... Processing helix chain 'A' and resid 34 through 51 removed outlier: 3.853A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.851A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 212 through 233 removed outlier: 3.952A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.616A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.943A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.874A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.749A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.619A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.817A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.761A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 482 Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.642A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.521A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.606A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.908A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 864 removed outlier: 3.636A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 981 removed outlier: 3.590A pdb=" N GLN C 955 " --> pdb=" O MET C 951 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.566A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 998 removed outlier: 4.015A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.710A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.688A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 Processing helix chain 'C' and resid 1137 through 1151 Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.699A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1333 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 113 through 119 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.641A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 3.891A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 309 removed outlier: 3.506A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 370 through 388 Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 504 through 515 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 613 through 636 Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.719A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.744A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.715A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 935 removed outlier: 3.671A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Proline residue: D 926 - end of helix removed outlier: 3.501A pdb=" N THR D 931 " --> pdb=" O GLY D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1147 removed outlier: 3.864A pdb=" N ARG D1140 " --> pdb=" O GLY D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.633A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.573A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.364A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1293 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.653A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1373 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.518A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 70 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 8.731A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.511A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLY A 151 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 105 Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.564A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 17 removed outlier: 3.888A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 8.164A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.869A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.182A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.182A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.493A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB8, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.241A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.721A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.817A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'C' and resid 623 through 624 removed outlier: 4.307A pdb=" N HIS C 628 " --> pdb=" O ASP C 624 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.533A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.046A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.355A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.862A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.257A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD3, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.548A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.468A pdb=" N GLN D 158 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD6, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AD7, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AD8, first strand: chain 'D' and resid 957 through 961 removed outlier: 4.003A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 966 through 967 removed outlier: 4.050A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 1035 through 1038 Processing sheet with id=AE2, first strand: chain 'D' and resid 1059 through 1061 removed outlier: 3.896A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1163 through 1165 removed outlier: 4.475A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1277 through 1279 1087 hydrogen bonds defined for protein. 3078 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 7.65 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8805 1.34 - 1.47: 5846 1.47 - 1.60: 11876 1.60 - 1.73: 76 1.73 - 1.86: 186 Bond restraints: 26789 Sorted by residual: bond pdb=" C2 2TM D2004 " pdb=" O2 2TM D2004 " ideal model delta sigma weight residual 1.235 1.392 -0.157 2.00e-02 2.50e+03 6.17e+01 bond pdb=" C4 2TM D2004 " pdb=" N4 2TM D2004 " ideal model delta sigma weight residual 1.342 1.452 -0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C2' 2TM D2004 " pdb=" C3' 2TM D2004 " ideal model delta sigma weight residual 1.543 1.443 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C3' DT T 24 " pdb=" O3' DT T 24 " ideal model delta sigma weight residual 1.435 1.371 0.064 1.30e-02 5.92e+03 2.39e+01 bond pdb=" C1' 2TM D2004 " pdb=" O4' 2TM D2004 " ideal model delta sigma weight residual 1.409 1.501 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 26784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 36010 3.75 - 7.49: 401 7.49 - 11.24: 43 11.24 - 14.98: 4 14.98 - 18.73: 2 Bond angle restraints: 36460 Sorted by residual: angle pdb=" CA PRO D 758 " pdb=" N PRO D 758 " pdb=" CD PRO D 758 " ideal model delta sigma weight residual 112.00 100.93 11.07 1.40e+00 5.10e-01 6.25e+01 angle pdb=" CB ARG B 170 " pdb=" CG ARG B 170 " pdb=" CD ARG B 170 " ideal model delta sigma weight residual 111.30 126.72 -15.42 2.30e+00 1.89e-01 4.49e+01 angle pdb=" N GLU B 226 " pdb=" CA GLU B 226 " pdb=" CB GLU B 226 " ideal model delta sigma weight residual 110.12 119.67 -9.55 1.47e+00 4.63e-01 4.22e+01 angle pdb=" CB ARG C 542 " pdb=" CG ARG C 542 " pdb=" CD ARG C 542 " ideal model delta sigma weight residual 111.30 96.75 14.55 2.30e+00 1.89e-01 4.00e+01 angle pdb=" O4' DG T 12 " pdb=" C4' DG T 12 " pdb=" C3' DG T 12 " ideal model delta sigma weight residual 106.00 102.33 3.67 6.00e-01 2.78e+00 3.74e+01 ... (remaining 36455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.06: 15223 28.06 - 56.13: 968 56.13 - 84.19: 124 84.19 - 112.25: 8 112.25 - 140.31: 1 Dihedral angle restraints: 16324 sinusoidal: 7157 harmonic: 9167 Sorted by residual: dihedral pdb=" CA LYS C 236 " pdb=" C LYS C 236 " pdb=" N LEU C 237 " pdb=" CA LEU C 237 " ideal model delta harmonic sigma weight residual 180.00 139.10 40.90 0 5.00e+00 4.00e-02 6.69e+01 dihedral pdb=" CA THR C 595 " pdb=" C THR C 595 " pdb=" N ASP C 596 " pdb=" CA ASP C 596 " ideal model delta harmonic sigma weight residual -180.00 -142.26 -37.74 0 5.00e+00 4.00e-02 5.70e+01 dihedral pdb=" CA ASP D1184 " pdb=" C ASP D1184 " pdb=" N PRO D1185 " pdb=" CA PRO D1185 " ideal model delta harmonic sigma weight residual -180.00 -145.28 -34.72 0 5.00e+00 4.00e-02 4.82e+01 ... (remaining 16321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3774 0.097 - 0.193: 354 0.193 - 0.290: 33 0.290 - 0.387: 4 0.387 - 0.483: 1 Chirality restraints: 4166 Sorted by residual: chirality pdb=" CB VAL C 913 " pdb=" CA VAL C 913 " pdb=" CG1 VAL C 913 " pdb=" CG2 VAL C 913 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CA ARG B 170 " pdb=" N ARG B 170 " pdb=" C ARG B 170 " pdb=" CB ARG B 170 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CG LEU D 478 " pdb=" CB LEU D 478 " pdb=" CD1 LEU D 478 " pdb=" CD2 LEU D 478 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 4163 not shown) Planarity restraints: 4557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 757 " -0.141 5.00e-02 4.00e+02 2.05e-01 6.71e+01 pdb=" N PRO D 758 " 0.353 5.00e-02 4.00e+02 pdb=" CA PRO D 758 " -0.119 5.00e-02 4.00e+02 pdb=" CD PRO D 758 " -0.094 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 514 " 0.038 2.00e-02 2.50e+03 3.04e-02 1.61e+01 pdb=" CG PHE C 514 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE C 514 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 514 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 514 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 514 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 514 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 287 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO D 288 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO D 288 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 288 " 0.055 5.00e-02 4.00e+02 ... (remaining 4554 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.00: 5 2.00 - 2.72: 1898 2.72 - 3.45: 39372 3.45 - 4.17: 63167 4.17 - 4.90: 111988 Nonbonded interactions: 216430 Sorted by model distance: nonbonded pdb=" ND2 ASN D 910 " pdb=" O ASN E 15 " model vdw 1.275 3.120 nonbonded pdb=" OE1 GLU D 418 " pdb=" CG2 VAL E 48 " model vdw 1.523 3.460 nonbonded pdb=" ND2 ASN D 910 " pdb=" C ASN E 15 " model vdw 1.632 3.350 nonbonded pdb=" ND2 ASN D 910 " pdb=" OD1 ASN E 15 " model vdw 1.740 3.120 nonbonded pdb=" ND2 ASN D 910 " pdb=" CA ASN E 15 " model vdw 1.800 3.550 ... (remaining 216425 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 'A' and resid 7 through 235) selection = (chain 'B' and resid 7 through 235) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 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: 0.050 Process input model: 33.580 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.008 0.372 26797 Z= 0.374 Angle : 1.070 18.727 36472 Z= 0.605 Chirality : 0.060 0.483 4166 Planarity : 0.007 0.205 4557 Dihedral : 17.097 140.312 10428 Min Nonbonded Distance : 1.275 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.93 % Favored : 91.60 % Rotamer: Outliers : 1.22 % Allowed : 1.29 % Favored : 97.49 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.13 % 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: -2.39 (0.13), residues: 3178 helix: -0.54 (0.14), residues: 1119 sheet: -1.03 (0.24), residues: 393 loop : -2.55 (0.12), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 170 TYR 0.041 0.003 TYR D 555 PHE 0.069 0.003 PHE C 514 TRP 0.026 0.003 TRP D1020 HIS 0.017 0.002 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.36 (26789) covalent geometry : angle 1.06999 / 0.61 (36460) hydrogen bonds : bond 0.13601 / 9.39 ( 1128) hydrogen bonds : angle 6.67559 / 4.68 ( 3190) metal coordination : bond 0.17571 / 8.03 ( 8) metal coordination : angle 1.34292 / 0.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 396 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 CYS cc_start: 0.7461 (m) cc_final: 0.7106 (m) REVERT: B 142 MET cc_start: 0.7960 (ptp) cc_final: 0.7672 (ptp) REVERT: C 104 ILE cc_start: 0.6244 (OUTLIER) cc_final: 0.5613 (mt) REVERT: C 1119 MET cc_start: 0.8525 (tpt) cc_final: 0.8310 (tpt) REVERT: D 604 MET cc_start: 0.8362 (ttm) cc_final: 0.8153 (ttp) REVERT: D 739 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7973 (mm-40) REVERT: D 1175 LEU cc_start: 0.6593 (mt) cc_final: 0.6161 (tt) outliers start: 33 outliers final: 2 residues processed: 417 average time/residue: 0.2019 time to fit residues: 130.3400 Evaluate side-chains 278 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 275 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain D residue 1301 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.0870 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 462 ASN C 659 GLN C 677 ASN C 761 GLN C 808 ASN C 932 GLN C1023 HIS ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN C1313 HIS D 157 GLN D 276 ASN D 458 ASN D 861 ASN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.186934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.144168 restraints weight = 34415.889| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.11 r_work: 0.3513 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26797 Z= 0.182 Angle : 0.769 12.581 36472 Z= 0.396 Chirality : 0.047 0.324 4166 Planarity : 0.006 0.091 4557 Dihedral : 13.699 138.612 4207 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.88 % Favored : 94.02 % Rotamer: Outliers : 1.18 % Allowed : 10.18 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.23 (0.14), residues: 3178 helix: 0.72 (0.15), residues: 1132 sheet: -0.64 (0.24), residues: 397 loop : -2.04 (0.13), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 88 TYR 0.028 0.002 TYR C 62 PHE 0.027 0.002 PHE C 514 TRP 0.013 0.002 TRP D 580 HIS 0.011 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (26789) covalent geometry : angle 0.76754 / 0.40 (36460) hydrogen bonds : bond 0.05068 / 3.47 ( 1128) hydrogen bonds : angle 5.29390 / 3.71 ( 3190) metal coordination : bond 0.01339 / 0.59 ( 8) metal coordination : angle 3.08011 / 1.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 313 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 CYS cc_start: 0.8154 (m) cc_final: 0.7769 (m) REVERT: B 193 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: B 199 ASP cc_start: 0.6868 (p0) cc_final: 0.6458 (p0) REVERT: B 226 GLU cc_start: 0.7608 (pt0) cc_final: 0.7272 (mm-30) REVERT: C 542 ARG cc_start: 0.8041 (tpp-160) cc_final: 0.7813 (mmt180) REVERT: D 475 GLU cc_start: 0.8015 (mp0) cc_final: 0.7733 (mp0) REVERT: D 1040 MET cc_start: 0.2100 (tmm) cc_final: 0.1032 (tmm) REVERT: D 1175 LEU cc_start: 0.6708 (mt) cc_final: 0.6461 (mt) outliers start: 32 outliers final: 21 residues processed: 334 average time/residue: 0.1766 time to fit residues: 93.0017 Evaluate side-chains 287 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 265 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 752 ASN Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1313 HIS Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1301 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 72 optimal weight: 0.9980 chunk 271 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 284 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 29 optimal weight: 20.0000 chunk 84 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN A 194 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 490 GLN C 799 ASN C 834 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN C1313 HIS D 157 GLN D 424 ASN D 861 ASN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1108 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.185657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.142715 restraints weight = 34452.302| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.04 r_work: 0.3504 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 26797 Z= 0.173 Angle : 0.688 12.743 36472 Z= 0.355 Chirality : 0.045 0.329 4166 Planarity : 0.005 0.061 4557 Dihedral : 13.472 138.914 4205 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.14 % Favored : 93.71 % Rotamer: Outliers : 2.06 % Allowed : 13.31 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.89 (0.14), residues: 3178 helix: 0.94 (0.15), residues: 1144 sheet: -0.49 (0.24), residues: 390 loop : -1.80 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1223 TYR 0.020 0.002 TYR D 46 PHE 0.023 0.002 PHE C 514 TRP 0.010 0.001 TRP D 580 HIS 0.011 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (26789) covalent geometry : angle 0.68714 / 0.36 (36460) hydrogen bonds : bond 0.04665 / 3.19 ( 1128) hydrogen bonds : angle 4.96825 / 3.49 ( 3190) metal coordination : bond 0.00864 / 0.40 ( 8) metal coordination : angle 2.47246 / 1.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 303 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.6547 (t80) REVERT: B 54 CYS cc_start: 0.8264 (m) cc_final: 0.7906 (m) REVERT: B 142 MET cc_start: 0.8617 (ptp) cc_final: 0.8220 (ptp) REVERT: B 152 TYR cc_start: 0.8808 (t80) cc_final: 0.8515 (t80) REVERT: B 193 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: B 199 ASP cc_start: 0.7005 (p0) cc_final: 0.6501 (p0) REVERT: B 226 GLU cc_start: 0.7923 (pt0) cc_final: 0.7357 (mm-30) REVERT: C 121 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.5784 (pp20) REVERT: C 353 VAL cc_start: 0.8613 (t) cc_final: 0.8385 (p) REVERT: C 514 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7961 (m-10) REVERT: C 542 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.8027 (mmt180) REVERT: C 834 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7810 (mp-120) REVERT: C 947 GLU cc_start: 0.4368 (OUTLIER) cc_final: 0.3348 (tt0) REVERT: D 214 ARG cc_start: 0.7722 (ttm110) cc_final: 0.7481 (ttm110) REVERT: D 332 LYS cc_start: 0.8657 (ptmm) cc_final: 0.8204 (pttt) REVERT: D 475 GLU cc_start: 0.8267 (mp0) cc_final: 0.7930 (mp0) REVERT: D 905 ARG cc_start: 0.6696 (OUTLIER) cc_final: 0.6091 (ptm160) REVERT: D 1040 MET cc_start: 0.2167 (tmm) cc_final: 0.1314 (tmm) REVERT: D 1108 GLN cc_start: 0.2402 (OUTLIER) cc_final: 0.2141 (tp40) REVERT: D 1173 ARG cc_start: 0.6036 (tmm-80) cc_final: 0.4753 (ptp-110) REVERT: D 1349 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7703 (pm20) outliers start: 56 outliers final: 28 residues processed: 345 average time/residue: 0.1853 time to fit residues: 100.1457 Evaluate side-chains 306 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 268 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 752 ASN Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1313 HIS Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1108 GLN Chi-restraints excluded: chain D residue 1301 THR Chi-restraints excluded: chain D residue 1349 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 96 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 322 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 190 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 618 GLN C 799 ASN C 834 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN C1313 HIS D 861 ASN ** D 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1108 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.184309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.141289 restraints weight = 34296.421| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.02 r_work: 0.3476 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 26797 Z= 0.180 Angle : 0.668 13.366 36472 Z= 0.346 Chirality : 0.044 0.327 4166 Planarity : 0.005 0.059 4557 Dihedral : 13.379 138.956 4205 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.01 % Favored : 93.90 % Rotamer: Outliers : 2.77 % Allowed : 14.49 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.71 (0.14), residues: 3178 helix: 0.98 (0.15), residues: 1152 sheet: -0.26 (0.25), residues: 384 loop : -1.65 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1223 TYR 0.019 0.002 TYR D 46 PHE 0.027 0.002 PHE C 514 TRP 0.007 0.001 TRP D 580 HIS 0.011 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (26789) covalent geometry : angle 0.66702 / 0.35 (36460) hydrogen bonds : bond 0.04462 / 3.04 ( 1128) hydrogen bonds : angle 4.84676 / 3.41 ( 3190) metal coordination : bond 0.00665 / 0.33 ( 8) metal coordination : angle 2.21681 / 1.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 293 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.7854 (m110) REVERT: A 122 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8179 (mt-10) REVERT: A 231 PHE cc_start: 0.6991 (OUTLIER) cc_final: 0.6664 (t80) REVERT: B 51 MET cc_start: 0.9162 (mmm) cc_final: 0.8935 (mmm) REVERT: B 54 CYS cc_start: 0.8223 (m) cc_final: 0.7852 (m) REVERT: B 142 MET cc_start: 0.8519 (ptp) cc_final: 0.8130 (ptp) REVERT: B 152 TYR cc_start: 0.8806 (t80) cc_final: 0.8460 (t80) REVERT: B 193 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6719 (tt0) REVERT: B 199 ASP cc_start: 0.7096 (p0) cc_final: 0.6373 (p0) REVERT: B 226 GLU cc_start: 0.8049 (pt0) cc_final: 0.7533 (mm-30) REVERT: C 121 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.5868 (pp20) REVERT: C 353 VAL cc_start: 0.8506 (t) cc_final: 0.8296 (p) REVERT: C 490 GLN cc_start: 0.7166 (tt0) cc_final: 0.6647 (tp-100) REVERT: C 514 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8220 (m-10) REVERT: C 542 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7744 (mmt-90) REVERT: C 947 GLU cc_start: 0.4409 (OUTLIER) cc_final: 0.3423 (tt0) REVERT: C 1164 PHE cc_start: 0.7760 (m-10) cc_final: 0.7358 (m-10) REVERT: D 69 GLU cc_start: 0.7566 (pp20) cc_final: 0.7142 (mt-10) REVERT: D 332 LYS cc_start: 0.8583 (ptmm) cc_final: 0.8092 (pttt) REVERT: D 475 GLU cc_start: 0.8280 (mp0) cc_final: 0.7879 (mp0) REVERT: D 905 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.6276 (ptm160) REVERT: D 1040 MET cc_start: 0.2087 (tmm) cc_final: 0.1212 (tmm) REVERT: D 1173 ARG cc_start: 0.6386 (tmm-80) cc_final: 0.4683 (ptp-110) REVERT: D 1325 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.6531 (p90) outliers start: 75 outliers final: 42 residues processed: 349 average time/residue: 0.1853 time to fit residues: 102.7018 Evaluate side-chains 316 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 265 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 752 ASN Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1301 THR Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1349 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 196 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 132 optimal weight: 0.0670 chunk 127 optimal weight: 3.9990 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN C 214 ASN C 437 ASN ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN C 799 ASN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 45 ASN D 861 ASN D1108 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.181221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.139825 restraints weight = 34105.869| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.05 r_work: 0.3439 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 26797 Z= 0.230 Angle : 0.695 12.866 36472 Z= 0.359 Chirality : 0.045 0.368 4166 Planarity : 0.005 0.084 4557 Dihedral : 13.364 137.361 4205 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.48 % Favored : 93.42 % Rotamer: Outliers : 2.80 % Allowed : 15.34 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.14), residues: 3178 helix: 0.93 (0.15), residues: 1152 sheet: -0.21 (0.26), residues: 373 loop : -1.55 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 170 TYR 0.018 0.002 TYR D 772 PHE 0.033 0.002 PHE C 514 TRP 0.010 0.001 TRP D 236 HIS 0.014 0.002 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (26789) covalent geometry : angle 0.69369 / 0.36 (36460) hydrogen bonds : bond 0.04604 / 3.15 ( 1128) hydrogen bonds : angle 4.83062 / 3.40 ( 3190) metal coordination : bond 0.00873 / 0.44 ( 8) metal coordination : angle 2.26559 / 1.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 274 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8385 (OUTLIER) cc_final: 0.7924 (m110) REVERT: A 231 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.6772 (t80) REVERT: B 51 MET cc_start: 0.9175 (mmm) cc_final: 0.8947 (mmm) REVERT: B 152 TYR cc_start: 0.8782 (t80) cc_final: 0.8407 (t80) REVERT: B 193 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6639 (tt0) REVERT: B 226 GLU cc_start: 0.8084 (pt0) cc_final: 0.7504 (mm-30) REVERT: C 65 ASN cc_start: 0.6569 (p0) cc_final: 0.5836 (p0) REVERT: C 121 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6541 (pp20) REVERT: C 353 VAL cc_start: 0.8493 (t) cc_final: 0.8278 (p) REVERT: C 461 GLU cc_start: 0.8567 (tt0) cc_final: 0.8329 (tt0) REVERT: C 490 GLN cc_start: 0.6896 (tt0) cc_final: 0.6458 (tp-100) REVERT: C 514 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.8108 (m-10) REVERT: C 542 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7955 (mmt180) REVERT: C 800 MET cc_start: 0.8660 (mtp) cc_final: 0.8435 (mmm) REVERT: C 947 GLU cc_start: 0.4466 (OUTLIER) cc_final: 0.3559 (tt0) REVERT: D 69 GLU cc_start: 0.7701 (pp20) cc_final: 0.7217 (mt-10) REVERT: D 214 ARG cc_start: 0.7562 (ttm110) cc_final: 0.7355 (ttm110) REVERT: D 332 LYS cc_start: 0.8611 (ptmm) cc_final: 0.8154 (pttt) REVERT: D 475 GLU cc_start: 0.8304 (mp0) cc_final: 0.7943 (mp0) REVERT: D 1040 MET cc_start: 0.1932 (tmm) cc_final: 0.1189 (tmm) REVERT: D 1095 MET cc_start: -0.0431 (ttt) cc_final: -0.0701 (ppp) REVERT: D 1173 ARG cc_start: 0.6319 (tmm-80) cc_final: 0.4586 (ptp-110) REVERT: D 1190 ILE cc_start: 0.6592 (mp) cc_final: 0.6189 (mp) REVERT: D 1205 GLU cc_start: 0.7140 (mp0) cc_final: 0.6678 (tp30) REVERT: D 1325 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.6560 (p90) outliers start: 76 outliers final: 44 residues processed: 331 average time/residue: 0.1837 time to fit residues: 96.7054 Evaluate side-chains 309 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 257 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1301 THR Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1325 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 234 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 90 optimal weight: 0.0270 chunk 235 optimal weight: 0.1980 chunk 317 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 151 optimal weight: 0.0010 chunk 27 optimal weight: 3.9990 chunk 300 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 overall best weight: 0.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN C 41 GLN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 45 ASN D 158 GLN D 861 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.186680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.145232 restraints weight = 34363.211| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.08 r_work: 0.3514 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26797 Z= 0.126 Angle : 0.618 13.030 36472 Z= 0.319 Chirality : 0.043 0.291 4166 Planarity : 0.005 0.060 4557 Dihedral : 13.283 140.924 4205 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.76 % Favored : 94.15 % Rotamer: Outliers : 2.58 % Allowed : 16.59 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.15), residues: 3178 helix: 1.17 (0.15), residues: 1145 sheet: -0.15 (0.26), residues: 383 loop : -1.42 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 779 TYR 0.017 0.001 TYR D 46 PHE 0.022 0.001 PHE C 514 TRP 0.006 0.001 TRP D 115 HIS 0.005 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (26789) covalent geometry : angle 0.61663 / 0.32 (36460) hydrogen bonds : bond 0.04019 / 2.73 ( 1128) hydrogen bonds : angle 4.63944 / 3.26 ( 3190) metal coordination : bond 0.00387 / 0.18 ( 8) metal coordination : angle 2.08811 / 1.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 298 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8075 (mt-10) REVERT: A 231 PHE cc_start: 0.6919 (OUTLIER) cc_final: 0.6664 (t80) REVERT: B 127 GLN cc_start: 0.8398 (pm20) cc_final: 0.8025 (pm20) REVERT: B 142 MET cc_start: 0.8539 (ptp) cc_final: 0.8165 (ptp) REVERT: B 152 TYR cc_start: 0.8738 (t80) cc_final: 0.8345 (t80) REVERT: B 185 TYR cc_start: 0.8674 (p90) cc_final: 0.8314 (p90) REVERT: B 193 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6645 (tt0) REVERT: B 226 GLU cc_start: 0.7978 (pt0) cc_final: 0.7386 (mm-30) REVERT: B 231 PHE cc_start: 0.8551 (m-80) cc_final: 0.8178 (m-80) REVERT: C 121 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.5790 (pp20) REVERT: C 514 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8199 (m-10) REVERT: C 542 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7971 (mmt180) REVERT: C 947 GLU cc_start: 0.4298 (OUTLIER) cc_final: 0.3420 (tt0) REVERT: D 69 GLU cc_start: 0.7661 (pp20) cc_final: 0.7086 (mp0) REVERT: D 214 ARG cc_start: 0.7547 (ttm110) cc_final: 0.7298 (ttm110) REVERT: D 332 LYS cc_start: 0.8564 (ptmm) cc_final: 0.8138 (pttt) REVERT: D 475 GLU cc_start: 0.8234 (mp0) cc_final: 0.7861 (mp0) REVERT: D 545 HIS cc_start: 0.8484 (OUTLIER) cc_final: 0.7699 (p-80) REVERT: D 905 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.6147 (ptm160) REVERT: D 1040 MET cc_start: 0.1878 (tmm) cc_final: 0.1042 (tmm) REVERT: D 1173 ARG cc_start: 0.6667 (tmm-80) cc_final: 0.4883 (ptp-110) REVERT: D 1190 ILE cc_start: 0.6470 (mp) cc_final: 0.6109 (mp) REVERT: D 1205 GLU cc_start: 0.7180 (mp0) cc_final: 0.6704 (tp30) REVERT: D 1325 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.6766 (p90) outliers start: 70 outliers final: 48 residues processed: 351 average time/residue: 0.1880 time to fit residues: 104.0663 Evaluate side-chains 321 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 264 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1301 THR Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1349 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 64 optimal weight: 4.9990 chunk 238 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 chunk 296 optimal weight: 1.9990 chunk 313 optimal weight: 10.0000 chunk 270 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 297 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 861 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.183578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.140705 restraints weight = 34203.804| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.01 r_work: 0.3456 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26797 Z= 0.190 Angle : 0.649 13.284 36472 Z= 0.334 Chirality : 0.044 0.322 4166 Planarity : 0.005 0.060 4557 Dihedral : 13.233 139.445 4205 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.10 % Favored : 93.77 % Rotamer: Outliers : 2.69 % Allowed : 16.78 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.42 (0.15), residues: 3178 helix: 1.14 (0.15), residues: 1145 sheet: -0.12 (0.27), residues: 362 loop : -1.38 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 314 TYR 0.023 0.002 TYR C1229 PHE 0.030 0.002 PHE C 514 TRP 0.008 0.001 TRP D 236 HIS 0.010 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (26789) covalent geometry : angle 0.64774 / 0.33 (36460) hydrogen bonds : bond 0.04234 / 2.89 ( 1128) hydrogen bonds : angle 4.65236 / 3.27 ( 3190) metal coordination : bond 0.00655 / 0.33 ( 8) metal coordination : angle 2.03844 / 1.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 273 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7891 (mm110) REVERT: A 231 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6763 (t80) REVERT: B 7 GLU cc_start: 0.4903 (OUTLIER) cc_final: 0.4023 (pm20) REVERT: B 142 MET cc_start: 0.8509 (ptp) cc_final: 0.8154 (ptp) REVERT: B 152 TYR cc_start: 0.8771 (t80) cc_final: 0.8383 (t80) REVERT: B 185 TYR cc_start: 0.8738 (p90) cc_final: 0.8389 (p90) REVERT: B 193 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6686 (tt0) REVERT: B 226 GLU cc_start: 0.8083 (pt0) cc_final: 0.7476 (mm-30) REVERT: C 370 MET cc_start: 0.7767 (mmm) cc_final: 0.7134 (mmm) REVERT: C 514 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8083 (m-10) REVERT: C 542 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8039 (mmt180) REVERT: C 947 GLU cc_start: 0.4378 (OUTLIER) cc_final: 0.3593 (tt0) REVERT: C 1296 ASP cc_start: 0.9120 (OUTLIER) cc_final: 0.8629 (t0) REVERT: D 69 GLU cc_start: 0.7714 (pp20) cc_final: 0.7126 (mp0) REVERT: D 332 LYS cc_start: 0.8575 (ptmm) cc_final: 0.8193 (pttt) REVERT: D 475 GLU cc_start: 0.8272 (mp0) cc_final: 0.7988 (mp0) REVERT: D 545 HIS cc_start: 0.8628 (OUTLIER) cc_final: 0.7875 (p-80) REVERT: D 832 LYS cc_start: 0.7919 (mmtm) cc_final: 0.7530 (mptt) REVERT: D 1040 MET cc_start: 0.1852 (tmm) cc_final: 0.1013 (tmm) REVERT: D 1173 ARG cc_start: 0.6691 (tmm-80) cc_final: 0.4837 (ptp-110) REVERT: D 1190 ILE cc_start: 0.6433 (mp) cc_final: 0.6035 (mp) REVERT: D 1205 GLU cc_start: 0.7257 (mp0) cc_final: 0.6616 (tp30) REVERT: D 1325 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.6650 (p90) outliers start: 73 outliers final: 53 residues processed: 328 average time/residue: 0.1888 time to fit residues: 98.3990 Evaluate side-chains 328 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 265 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1172 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1281 GLU Chi-restraints excluded: chain D residue 1301 THR Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1349 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 6 optimal weight: 4.9990 chunk 179 optimal weight: 0.5980 chunk 288 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 318 optimal weight: 30.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 266 ASN D 861 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.184176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.141430 restraints weight = 34200.725| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.92 r_work: 0.3475 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26797 Z= 0.157 Angle : 0.638 13.294 36472 Z= 0.328 Chirality : 0.044 0.651 4166 Planarity : 0.005 0.060 4557 Dihedral : 13.191 139.897 4205 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.10 % Favored : 93.77 % Rotamer: Outliers : 2.69 % Allowed : 17.29 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.36 (0.15), residues: 3178 helix: 1.14 (0.15), residues: 1153 sheet: -0.16 (0.26), residues: 371 loop : -1.29 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 314 TYR 0.022 0.001 TYR C1229 PHE 0.028 0.001 PHE C 514 TRP 0.007 0.001 TRP D 236 HIS 0.007 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (26789) covalent geometry : angle 0.63753 / 0.33 (36460) hydrogen bonds : bond 0.04091 / 2.78 ( 1128) hydrogen bonds : angle 4.61463 / 3.24 ( 3190) metal coordination : bond 0.00581 / 0.29 ( 8) metal coordination : angle 1.89622 / 1.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 274 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: A 231 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.6787 (t80) REVERT: B 7 GLU cc_start: 0.4915 (OUTLIER) cc_final: 0.4038 (pm20) REVERT: B 127 GLN cc_start: 0.8358 (pm20) cc_final: 0.7896 (pm20) REVERT: B 142 MET cc_start: 0.8500 (ptp) cc_final: 0.8117 (ptp) REVERT: B 152 TYR cc_start: 0.8745 (t80) cc_final: 0.8337 (t80) REVERT: B 185 TYR cc_start: 0.8722 (p90) cc_final: 0.8381 (p90) REVERT: B 193 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6701 (tt0) REVERT: B 226 GLU cc_start: 0.8055 (pt0) cc_final: 0.7444 (mm-30) REVERT: B 231 PHE cc_start: 0.8639 (m-80) cc_final: 0.8355 (m-80) REVERT: C 353 VAL cc_start: 0.8577 (t) cc_final: 0.8368 (p) REVERT: C 398 SER cc_start: 0.7882 (OUTLIER) cc_final: 0.7619 (m) REVERT: C 514 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8065 (m-10) REVERT: C 542 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7993 (mmt180) REVERT: C 947 GLU cc_start: 0.4385 (OUTLIER) cc_final: 0.3638 (tt0) REVERT: C 1296 ASP cc_start: 0.9077 (OUTLIER) cc_final: 0.8438 (t0) REVERT: D 69 GLU cc_start: 0.7713 (pp20) cc_final: 0.7187 (mt-10) REVERT: D 214 ARG cc_start: 0.7510 (ttm110) cc_final: 0.7242 (ttm110) REVERT: D 332 LYS cc_start: 0.8578 (ptmm) cc_final: 0.8167 (pttt) REVERT: D 475 GLU cc_start: 0.8259 (mp0) cc_final: 0.7977 (mp0) REVERT: D 545 HIS cc_start: 0.8636 (OUTLIER) cc_final: 0.7878 (p-80) REVERT: D 832 LYS cc_start: 0.7966 (mmtm) cc_final: 0.7446 (mptt) REVERT: D 1040 MET cc_start: 0.1839 (tmm) cc_final: 0.0964 (tmm) REVERT: D 1173 ARG cc_start: 0.6813 (tmm-80) cc_final: 0.4978 (ptp-110) REVERT: D 1190 ILE cc_start: 0.6426 (mp) cc_final: 0.6031 (mp) REVERT: D 1205 GLU cc_start: 0.7214 (mp0) cc_final: 0.6572 (tp30) REVERT: D 1325 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.6659 (p90) outliers start: 73 outliers final: 56 residues processed: 327 average time/residue: 0.1844 time to fit residues: 95.7018 Evaluate side-chains 324 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 257 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1281 GLU Chi-restraints excluded: chain D residue 1301 THR Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1349 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 92 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 181 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 112 optimal weight: 0.8980 chunk 230 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 164 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 309 ASN D 861 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.184091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141378 restraints weight = 34300.611| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.03 r_work: 0.3483 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26797 Z= 0.137 Angle : 0.620 13.452 36472 Z= 0.318 Chirality : 0.044 0.645 4166 Planarity : 0.005 0.060 4557 Dihedral : 13.072 140.836 4205 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.95 % Favored : 93.93 % Rotamer: Outliers : 2.58 % Allowed : 17.44 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.31 (0.15), residues: 3178 helix: 1.19 (0.15), residues: 1154 sheet: -0.14 (0.26), residues: 377 loop : -1.28 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 314 TYR 0.022 0.001 TYR C1229 PHE 0.027 0.001 PHE C 514 TRP 0.006 0.001 TRP D 236 HIS 0.014 0.001 HIS C1237 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (26789) covalent geometry : angle 0.61918 / 0.32 (36460) hydrogen bonds : bond 0.03941 / 2.68 ( 1128) hydrogen bonds : angle 4.55854 / 3.20 ( 3190) metal coordination : bond 0.00481 / 0.23 ( 8) metal coordination : angle 1.93424 / 1.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 268 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7534 (tt0) REVERT: A 231 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6893 (t80) REVERT: B 7 GLU cc_start: 0.4802 (OUTLIER) cc_final: 0.3987 (pm20) REVERT: B 127 GLN cc_start: 0.8324 (pm20) cc_final: 0.7957 (pm20) REVERT: B 152 TYR cc_start: 0.8684 (t80) cc_final: 0.8281 (t80) REVERT: B 185 TYR cc_start: 0.8593 (p90) cc_final: 0.8179 (p90) REVERT: B 193 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6608 (tt0) REVERT: B 226 GLU cc_start: 0.7865 (pt0) cc_final: 0.7377 (mm-30) REVERT: B 231 PHE cc_start: 0.8533 (m-80) cc_final: 0.8329 (m-10) REVERT: C 370 MET cc_start: 0.7734 (mmm) cc_final: 0.7183 (mmm) REVERT: C 398 SER cc_start: 0.7514 (OUTLIER) cc_final: 0.7165 (m) REVERT: C 514 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7842 (m-10) REVERT: C 542 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7908 (mmt180) REVERT: C 947 GLU cc_start: 0.4281 (OUTLIER) cc_final: 0.3606 (tt0) REVERT: C 1164 PHE cc_start: 0.7520 (m-10) cc_final: 0.7243 (m-10) REVERT: C 1296 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8161 (t0) REVERT: D 69 GLU cc_start: 0.7602 (pp20) cc_final: 0.7173 (mt-10) REVERT: D 332 LYS cc_start: 0.8378 (ptmm) cc_final: 0.8033 (pttt) REVERT: D 475 GLU cc_start: 0.8101 (mp0) cc_final: 0.7745 (mp0) REVERT: D 545 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.7762 (p-80) REVERT: D 832 LYS cc_start: 0.7979 (mmtm) cc_final: 0.7472 (mptt) REVERT: D 1149 ARG cc_start: 0.6820 (tpp-160) cc_final: 0.6343 (mmt180) REVERT: D 1173 ARG cc_start: 0.6801 (tmm-80) cc_final: 0.5042 (ptp-110) REVERT: D 1190 ILE cc_start: 0.6283 (mp) cc_final: 0.5943 (mp) REVERT: D 1205 GLU cc_start: 0.7237 (mp0) cc_final: 0.6584 (tp30) REVERT: D 1278 GLU cc_start: 0.7879 (pp20) cc_final: 0.7667 (pp20) REVERT: D 1325 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.6504 (p90) outliers start: 70 outliers final: 51 residues processed: 318 average time/residue: 0.1839 time to fit residues: 92.8555 Evaluate side-chains 321 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 259 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1281 GLU Chi-restraints excluded: chain D residue 1301 THR Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1349 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 309 optimal weight: 3.9990 chunk 189 optimal weight: 0.0570 chunk 315 optimal weight: 9.9990 chunk 182 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 209 optimal weight: 0.4980 chunk 242 optimal weight: 3.9990 chunk 318 optimal weight: 30.0000 chunk 196 optimal weight: 10.0000 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN B 41 ASN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 861 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.183342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.140706 restraints weight = 34229.126| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.04 r_work: 0.3471 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26797 Z= 0.154 Angle : 0.629 13.255 36472 Z= 0.323 Chirality : 0.044 0.618 4166 Planarity : 0.005 0.060 4557 Dihedral : 12.985 140.540 4205 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.98 % Favored : 93.90 % Rotamer: Outliers : 2.65 % Allowed : 17.51 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.30 (0.15), residues: 3178 helix: 1.20 (0.15), residues: 1152 sheet: -0.21 (0.26), residues: 383 loop : -1.25 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 214 TYR 0.025 0.002 TYR C1229 PHE 0.027 0.001 PHE C 514 TRP 0.010 0.001 TRP D 236 HIS 0.007 0.001 HIS C1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (26789) covalent geometry : angle 0.62847 / 0.32 (36460) hydrogen bonds : bond 0.03986 / 2.71 ( 1128) hydrogen bonds : angle 4.55807 / 3.20 ( 3190) metal coordination : bond 0.00567 / 0.28 ( 8) metal coordination : angle 1.97261 / 1.06 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 271 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: A 231 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6927 (t80) REVERT: B 7 GLU cc_start: 0.4891 (OUTLIER) cc_final: 0.4012 (pm20) REVERT: B 142 MET cc_start: 0.8563 (ptp) cc_final: 0.8186 (ptp) REVERT: B 152 TYR cc_start: 0.8753 (t80) cc_final: 0.8297 (t80) REVERT: B 185 TYR cc_start: 0.8730 (p90) cc_final: 0.8344 (p90) REVERT: B 193 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6700 (tt0) REVERT: B 226 GLU cc_start: 0.8113 (pt0) cc_final: 0.7424 (mm-30) REVERT: B 231 PHE cc_start: 0.8639 (m-80) cc_final: 0.8439 (m-10) REVERT: C 370 MET cc_start: 0.7738 (mmm) cc_final: 0.7154 (mmm) REVERT: C 398 SER cc_start: 0.7678 (OUTLIER) cc_final: 0.7315 (m) REVERT: C 514 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7850 (m-10) REVERT: C 542 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.8011 (mmt180) REVERT: C 614 TYR cc_start: 0.9006 (m-80) cc_final: 0.8738 (m-80) REVERT: C 754 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.9000 (p) REVERT: C 947 GLU cc_start: 0.4407 (OUTLIER) cc_final: 0.3627 (tt0) REVERT: C 1164 PHE cc_start: 0.7748 (m-10) cc_final: 0.7543 (m-10) REVERT: C 1296 ASP cc_start: 0.8891 (OUTLIER) cc_final: 0.8298 (t0) REVERT: D 332 LYS cc_start: 0.8515 (ptmm) cc_final: 0.8133 (pttt) REVERT: D 475 GLU cc_start: 0.8322 (mp0) cc_final: 0.8042 (mp0) REVERT: D 545 HIS cc_start: 0.8659 (OUTLIER) cc_final: 0.7946 (p-80) REVERT: D 812 ASP cc_start: 0.8663 (t70) cc_final: 0.8209 (t0) REVERT: D 1149 ARG cc_start: 0.6989 (tpp-160) cc_final: 0.6497 (mmt180) REVERT: D 1173 ARG cc_start: 0.6859 (tmm-80) cc_final: 0.5156 (ptp-110) REVERT: D 1190 ILE cc_start: 0.6514 (mp) cc_final: 0.6205 (mp) REVERT: D 1278 GLU cc_start: 0.8069 (pp20) cc_final: 0.7868 (pp20) REVERT: D 1325 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.6640 (p90) outliers start: 72 outliers final: 54 residues processed: 323 average time/residue: 0.1808 time to fit residues: 92.7691 Evaluate side-chains 329 residues out of total 2720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 263 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 947 GLU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1232 MET Chi-restraints excluded: chain C residue 1236 ASN Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 905 ARG Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1281 GLU Chi-restraints excluded: chain D residue 1301 THR Chi-restraints excluded: chain D residue 1314 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1349 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 221 optimal weight: 0.0570 chunk 83 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 253 optimal weight: 0.5980 chunk 156 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 93 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 861 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.185588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.143434 restraints weight = 34099.418| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.94 r_work: 0.3500 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26797 Z= 0.126 Angle : 0.614 13.291 36472 Z= 0.316 Chirality : 0.043 0.618 4166 Planarity : 0.005 0.060 4557 Dihedral : 12.933 141.455 4205 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.04 % Favored : 93.86 % Rotamer: Outliers : 2.54 % Allowed : 17.88 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.24 (0.15), residues: 3178 helix: 1.28 (0.15), residues: 1148 sheet: -0.20 (0.27), residues: 383 loop : -1.22 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 214 TYR 0.023 0.001 TYR C1229 PHE 0.024 0.001 PHE C 514 TRP 0.007 0.001 TRP D 236 HIS 0.019 0.001 HIS C1237 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (26789) covalent geometry : angle 0.61347 / 0.32 (36460) hydrogen bonds : bond 0.03829 / 2.60 ( 1128) hydrogen bonds : angle 4.50554 / 3.16 ( 3190) metal coordination : bond 0.00433 / 0.21 ( 8) metal coordination : angle 1.94365 / 1.04 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7588.98 seconds wall clock time: 130 minutes 24.76 seconds (7824.76 seconds total)