Starting phenix.real_space_refine on Wed Oct 28 00:23:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rh3_4882/10_2026/6rh3_4882.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rh3_4882/10_2026/6rh3_4882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rh3_4882/10_2026/6rh3_4882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rh3_4882/10_2026/6rh3_4882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rh3_4882/10_2026/6rh3_4882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rh3_4882/10_2026/6rh3_4882.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6rh3_4882/10_2026/6rh3_4882.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rh3_4882/10_2026/6rh3_4882.cif" } resolution = 3.6 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= 0.007 sd= 0.079 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 60 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16282 2.51 5 N 4657 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 6 residue(s): 0.22s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26300 Number of models: 1 Model: "" Number of chains: 9 Chain: "N" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 388 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain breaks: 1 Chain: "T" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 590 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "B" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1772 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219} Chain: "C" Number of atoms: 10407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10407 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1263} Chain breaks: 1 Chain: "D" Number of atoms: 10545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10545 Classifications: {'peptide': 1358} Link IDs: {'PTRANS': 55, 'TRANS': 1302} Chain: "E" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "R" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 216 Unusual residues: {'KAK': 1} Classifications: {'RNAv2': 9, 'undetermined': 1} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 7, None: 1} Not linked: pdbres=" U R 13 " pdbres="KAK R 14 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {' MG': 1, ' ZN': 2, 'CTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15374 SG CYS D 70 102.918 37.365 77.592 1.00116.84 S ATOM 15388 SG CYS D 72 103.790 34.166 77.715 1.00121.89 S ATOM 15496 SG CYS D 85 104.818 34.994 74.569 1.00114.80 S ATOM 15520 SG CYS D 88 101.436 36.270 74.655 1.00117.02 S ATOM 21208 SG CYS D 814 93.136 104.286 78.831 1.00 78.80 S ATOM 21773 SG CYS D 888 91.146 100.793 78.226 1.00 75.72 S ATOM 21824 SG CYS D 895 92.329 101.837 81.306 1.00 69.86 S ATOM 21845 SG CYS D 898 90.023 103.720 79.894 1.00 70.18 S Time building chain proxies: 5.50, per 1000 atoms: 0.21 Number of scatterers: 26300 At special positions: 0 Unit cell: (131.292, 146.922, 165.678, 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 60 15.00 Mg 1 11.99 O 5192 8.00 N 4657 7.00 C 16282 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " Number of angles added : 12 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5916 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 51 sheets defined 37.8% alpha, 14.4% beta 20 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.726A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 77 through 88 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 212 through 230 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.697A pdb=" N SER C 166 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 167' Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 291 through 295 Processing helix chain 'C' and resid 318 through 328 removed outlier: 4.461A pdb=" N SER C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) 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 387 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 481 removed outlier: 4.016A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.952A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.515A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 614 removed outlier: 3.913A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 614' 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 670 through 674 Processing helix chain 'C' and resid 675 through 688 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 738 through 741 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 859 through 864 removed outlier: 4.752A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 979 Processing helix chain 'C' and resid 985 through 991 Processing helix chain 'C' and resid 1006 through 1038 Processing helix chain 'C' and resid 1099 through 1103 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.711A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1151 Processing helix chain 'C' and resid 1167 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 1284 through 1292 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 34 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.593A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 263 through 283 Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.548A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.993A pdb=" N ALA D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 417 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 504 through 514 Processing helix chain 'D' and resid 529 through 540 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 613 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 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 802 Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 932 removed outlier: 3.733A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Proline residue: D 926 - end of helix Processing helix chain 'D' and resid 933 through 938 removed outlier: 4.172A pdb=" N ILE D 937 " --> pdb=" O THR D 934 " (cutoff:3.500A) Processing helix chain 'D' and resid 1068 through 1073 removed outlier: 4.680A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1147 removed outlier: 3.630A pdb=" N GLY D1137 " --> pdb=" O ASP D1133 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU D1138 " --> pdb=" O ILE D1134 " (cutoff:3.500A) Proline residue: D1139 - end of helix Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.563A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1319 through 1325 Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1360 through 1373 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 74 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 5.286A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 105 removed outlier: 6.191A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) 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: 6.780A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.830A 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 15 removed outlier: 3.658A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 3.654A pdb=" N MET B 142 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.099A 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: 7.063A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.287A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 453 removed outlier: 6.301A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'C' and resid 227 through 231 Processing sheet with id=AB8, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 256 Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 302 removed outlier: 6.944A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (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 599 through 603 removed outlier: 5.382A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 633 through 637 Processing sheet with id=AC5, first strand: chain 'C' and resid 717 through 718 removed outlier: 3.739A pdb=" N ASP C 781 " --> pdb=" O ALA C 718 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 749 through 752 removed outlier: 5.885A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC8, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC9, first strand: chain 'C' and resid 1065 through 1067 removed outlier: 4.878A pdb=" N LYS C1065 " --> pdb=" O LEU C1235 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C1098 " --> pdb=" O ALA C 803 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1065 through 1067 removed outlier: 4.878A pdb=" N LYS C1065 " --> pdb=" O LEU C1235 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 835 through 836 removed outlier: 3.632A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 835 through 836 removed outlier: 3.888A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.805A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AD6, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD7, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD8, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD9, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AE1, first strand: chain 'C' and resid 1336 through 1337 Processing sheet with id=AE2, first strand: chain 'D' and resid 103 through 112 removed outlier: 6.716A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AE4, first strand: chain 'D' and resid 547 through 556 Processing sheet with id=AE5, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE6, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE7, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE8, first strand: chain 'D' and resid 825 through 826 Processing sheet with id=AE9, first strand: chain 'D' and resid 848 through 850 removed outlier: 6.650A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASP D 855 " --> pdb=" O LYS D 850 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 957 through 961 Processing sheet with id=AF2, first strand: chain 'D' and resid 965 through 966 removed outlier: 3.947A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1098 through 1100 Processing sheet with id=AF4, first strand: chain 'D' and resid 1046 through 1050 Processing sheet with id=AF5, first strand: chain 'D' and resid 1187 through 1191 Processing sheet with id=AF6, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.709A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 1052 hydrogen bonds defined for protein. 2931 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 6.83 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7608 1.33 - 1.46: 5840 1.46 - 1.58: 13068 1.58 - 1.71: 109 1.71 - 1.83: 187 Bond restraints: 26812 Sorted by residual: bond pdb=" P KAK R 14 " pdb=" OP1 KAK R 14 " ideal model delta sigma weight residual 1.525 1.835 -0.310 2.00e-02 2.50e+03 2.40e+02 bond pdb=" P KAK R 14 " pdb=" OP2 KAK R 14 " ideal model delta sigma weight residual 1.534 1.835 -0.301 2.00e-02 2.50e+03 2.26e+02 bond pdb=" C5 KAK R 14 " pdb=" C4 KAK R 14 " ideal model delta sigma weight residual 1.368 1.470 -0.102 2.00e-02 2.50e+03 2.63e+01 bond pdb=" C3' DC T 20 " pdb=" O3' DC T 20 " ideal model delta sigma weight residual 1.435 1.374 0.061 1.30e-02 5.92e+03 2.22e+01 bond pdb=" N9 DA N 32 " pdb=" C4 DA N 32 " ideal model delta sigma weight residual 1.374 1.346 0.028 6.00e-03 2.78e+04 2.18e+01 ... (remaining 26807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 35388 2.68 - 5.35: 964 5.35 - 8.03: 85 8.03 - 10.70: 26 10.70 - 13.38: 3 Bond angle restraints: 36466 Sorted by residual: angle pdb=" O4' DC N 24 " pdb=" C4' DC N 24 " pdb=" C3' DC N 24 " ideal model delta sigma weight residual 106.00 101.65 4.35 6.00e-01 2.78e+00 5.26e+01 angle pdb=" O4' DT T 10 " pdb=" C4' DT T 10 " pdb=" C3' DT T 10 " ideal model delta sigma weight residual 106.00 102.19 3.81 6.00e-01 2.78e+00 4.03e+01 angle pdb=" O4' DT N 33 " pdb=" C4' DT N 33 " pdb=" C3' DT N 33 " ideal model delta sigma weight residual 106.00 102.21 3.79 6.00e-01 2.78e+00 3.98e+01 angle pdb=" C ARG D 362 " pdb=" N LEU D 363 " pdb=" CA LEU D 363 " ideal model delta sigma weight residual 122.31 109.90 12.41 2.00e+00 2.50e-01 3.85e+01 angle pdb=" C4' DT N 33 " pdb=" C3' DT N 33 " pdb=" C2' DT N 33 " ideal model delta sigma weight residual 103.10 98.46 4.64 9.00e-01 1.23e+00 2.66e+01 ... (remaining 36461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.98: 15885 28.98 - 57.96: 415 57.96 - 86.94: 52 86.94 - 115.92: 3 115.92 - 144.90: 4 Dihedral angle restraints: 16359 sinusoidal: 7157 harmonic: 9202 Sorted by residual: dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual 180.00 49.25 130.75 0 5.00e+00 4.00e-02 6.84e+02 dihedral pdb=" C4' G R 5 " pdb=" C3' G R 5 " pdb=" C2' G R 5 " pdb=" C1' G R 5 " ideal model delta sinusoidal sigma weight residual 36.34 -28.71 65.05 1 3.10e+00 1.04e-01 5.78e+02 dihedral pdb=" O4' G R 5 " pdb=" C4' G R 5 " pdb=" C3' G R 5 " pdb=" C2' G R 5 " ideal model delta sinusoidal sigma weight residual -35.15 20.66 -55.81 1 4.00e+00 6.25e-02 2.63e+02 ... (remaining 16356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2943 0.059 - 0.118: 1028 0.118 - 0.177: 164 0.177 - 0.236: 23 0.236 - 0.295: 4 Chirality restraints: 4162 Sorted by residual: chirality pdb=" C2' G R 5 " pdb=" C3' G R 5 " pdb=" O2' G R 5 " pdb=" C1' G R 5 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB ILE C 11 " pdb=" CA ILE C 11 " pdb=" CG1 ILE C 11 " pdb=" CG2 ILE C 11 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" P C R 6 " pdb=" OP1 C R 6 " pdb=" OP2 C R 6 " pdb=" O5' C R 6 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 4159 not shown) Planarity restraints: 4578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C1223 " -0.060 5.00e-02 4.00e+02 9.10e-02 1.32e+01 pdb=" N PRO C1224 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO C1224 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C1224 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 29 " -0.048 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO B 30 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 246 " -0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO D 247 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO D 247 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 247 " -0.038 5.00e-02 4.00e+02 ... (remaining 4575 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.82: 1 1.82 - 2.59: 319 2.59 - 3.36: 34209 3.36 - 4.13: 58843 4.13 - 4.90: 108220 Nonbonded interactions: 201592 Sorted by model distance: nonbonded pdb=" O2 DC N 35 " pdb=" N2 DG T 5 " model vdw 1.044 2.496 nonbonded pdb=" O2A CTP D1503 " pdb="MG MG D1504 " model vdw 1.861 2.170 nonbonded pdb=" O3B CTP D1503 " pdb="MG MG D1504 " model vdw 1.914 2.170 nonbonded pdb=" N2 DG N 31 " pdb=" O2 DC T 9 " model vdw 1.973 3.120 nonbonded pdb=" N2 DG N 29 " pdb=" O2 DC T 11 " model vdw 2.051 3.120 ... (remaining 201587 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 232) selection = (chain 'B' and resid 7 through 232) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 32.260 Find NCS groups from input model: 0.250 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 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 : 0.013 0.310 26821 Z= 0.601 Angle : 1.102 33.918 36478 Z= 0.595 Chirality : 0.058 0.295 4162 Planarity : 0.006 0.091 4578 Dihedral : 12.703 144.901 10443 Min Nonbonded Distance : 1.044 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.36 % Favored : 86.38 % Rotamer: Outliers : 0.11 % Allowed : 1.47 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.77 % 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: -4.23 (0.12), residues: 3195 helix: -1.91 (0.13), residues: 1108 sheet: -2.85 (0.22), residues: 402 loop : -3.53 (0.12), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 764 TYR 0.043 0.003 TYR C1229 PHE 0.037 0.003 PHE C 188 TRP 0.035 0.005 TRP D 115 HIS 0.011 0.003 HIS D 897 Details of bonding type rmsd/Z covalent geometry : bond 0.01284 / 0.60 (26812) covalent geometry : angle 1.05446 / 0.59 (36466) hydrogen bonds : bond 0.11322 / 12.37 ( 1091) hydrogen bonds : angle 6.75483 / 6.82 ( 3019) metal coordination : bond 0.09916 / 8.88 ( 8) metal coordination : angle 17.63379 / 33.20 ( 12) Misc. bond : bond 0.04089 / 1.64 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 535 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.8611 (tttt) cc_final: 0.8299 (tttp) REVERT: B 186 ASN cc_start: 0.8741 (m-40) cc_final: 0.8515 (m-40) REVERT: C 14 ASP cc_start: 0.8161 (t70) cc_final: 0.7955 (t0) REVERT: C 71 VAL cc_start: 0.8956 (t) cc_final: 0.8635 (t) REVERT: C 121 GLU cc_start: 0.7679 (pt0) cc_final: 0.7326 (pp20) REVERT: C 272 ARG cc_start: 0.5993 (mtt180) cc_final: 0.5575 (tmm-80) REVERT: C 311 CYS cc_start: 0.7057 (p) cc_final: 0.6719 (p) REVERT: C 391 SER cc_start: 0.9014 (t) cc_final: 0.8799 (m) REVERT: C 600 THR cc_start: 0.8861 (m) cc_final: 0.8341 (p) REVERT: C 601 ASP cc_start: 0.8080 (p0) cc_final: 0.7755 (p0) REVERT: C 681 MET cc_start: 0.8513 (mtp) cc_final: 0.8298 (mtt) REVERT: C 742 TYR cc_start: 0.7911 (m-10) cc_final: 0.7623 (m-10) REVERT: C 1119 MET cc_start: 0.7819 (tpt) cc_final: 0.7552 (tpt) REVERT: D 147 ILE cc_start: 0.8210 (pt) cc_final: 0.7874 (pt) REVERT: D 163 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7983 (mm-30) REVERT: D 267 ASP cc_start: 0.8036 (t0) cc_final: 0.7826 (t0) REVERT: D 1048 ARG cc_start: 0.8374 (tpt170) cc_final: 0.7765 (ttp-170) REVERT: D 1104 LYS cc_start: 0.7359 (mttt) cc_final: 0.7066 (pttm) REVERT: D 1208 ASP cc_start: 0.7721 (t0) cc_final: 0.7521 (t0) REVERT: E 8 ASP cc_start: 0.8496 (m-30) cc_final: 0.7898 (m-30) outliers start: 3 outliers final: 2 residues processed: 537 average time/residue: 0.1962 time to fit residues: 158.8610 Evaluate side-chains 272 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 270 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain E residue 63 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 132 HIS ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS C 510 GLN C 604 HIS ** C1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN C1220 GLN C1313 HIS D 232 ASN D 458 ASN D 875 ASN D 951 GLN D1218 HIS D1326 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.118648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.089274 restraints weight = 51716.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.092391 restraints weight = 25114.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.094381 restraints weight = 15969.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.095601 restraints weight = 12097.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096233 restraints weight = 10273.713| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26821 Z= 0.177 Angle : 0.786 24.762 36478 Z= 0.399 Chirality : 0.049 0.332 4162 Planarity : 0.006 0.077 4578 Dihedral : 14.584 140.231 4181 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.32 % Favored : 92.61 % Rotamer: Outliers : 1.72 % Allowed : 7.88 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % 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: -2.87 (0.13), residues: 3195 helix: -0.45 (0.15), residues: 1114 sheet: -2.19 (0.24), residues: 396 loop : -2.96 (0.13), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 69 TYR 0.028 0.002 TYR A 177 PHE 0.016 0.002 PHE C 514 TRP 0.014 0.002 TRP D 115 HIS 0.009 0.001 HIS D 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (26812) covalent geometry : angle 0.76459 / 0.40 (36466) hydrogen bonds : bond 0.06077 / 6.78 ( 1091) hydrogen bonds : angle 5.54805 / 5.58 ( 3019) metal coordination : bond 0.01093 / 1.05 ( 8) metal coordination : angle 10.10045 / 20.33 ( 12) Misc. bond : bond 0.00474 / 0.19 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 357 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.8377 (tttt) cc_final: 0.8017 (tttp) REVERT: A 181 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: B 80 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7471 (mt-10) REVERT: B 93 GLN cc_start: 0.8173 (tp40) cc_final: 0.7783 (mt0) REVERT: B 120 ASP cc_start: 0.8661 (p0) cc_final: 0.8449 (p0) REVERT: B 186 ASN cc_start: 0.8727 (m-40) cc_final: 0.8453 (m-40) REVERT: B 211 ILE cc_start: 0.8879 (tp) cc_final: 0.8617 (pt) REVERT: C 14 ASP cc_start: 0.8185 (t70) cc_final: 0.7960 (t0) REVERT: C 121 GLU cc_start: 0.7754 (pt0) cc_final: 0.7293 (pp20) REVERT: C 152 SER cc_start: 0.9448 (t) cc_final: 0.9226 (p) REVERT: C 315 MET cc_start: 0.7121 (mtp) cc_final: 0.6690 (mtp) REVERT: C 391 SER cc_start: 0.9093 (t) cc_final: 0.8726 (m) REVERT: C 600 THR cc_start: 0.8710 (m) cc_final: 0.8158 (p) REVERT: C 601 ASP cc_start: 0.7967 (p0) cc_final: 0.7697 (p0) REVERT: C 681 MET cc_start: 0.8310 (mtp) cc_final: 0.8015 (mtt) REVERT: C 965 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7465 (tm-30) REVERT: C 1194 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7981 (mt-10) REVERT: C 1304 MET cc_start: 0.9292 (tpp) cc_final: 0.8816 (tpp) REVERT: D 69 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7114 (tm-30) REVERT: D 111 THR cc_start: 0.9609 (m) cc_final: 0.9395 (p) REVERT: D 129 ASP cc_start: 0.8428 (t70) cc_final: 0.8038 (t70) REVERT: D 484 MET cc_start: 0.9035 (mtm) cc_final: 0.8824 (mtp) REVERT: D 582 ILE cc_start: 0.9090 (mt) cc_final: 0.8848 (tp) REVERT: D 932 MET cc_start: 0.8661 (mtm) cc_final: 0.8438 (mtp) REVERT: D 1048 ARG cc_start: 0.8353 (tpt170) cc_final: 0.7682 (ttp-170) REVERT: D 1104 LYS cc_start: 0.7388 (mttt) cc_final: 0.6967 (pttm) REVERT: E 8 ASP cc_start: 0.8213 (m-30) cc_final: 0.7656 (m-30) REVERT: E 55 GLU cc_start: 0.8238 (tt0) cc_final: 0.7992 (tt0) REVERT: E 69 ARG cc_start: 0.7497 (tpp-160) cc_final: 0.7259 (tpp-160) outliers start: 47 outliers final: 25 residues processed: 389 average time/residue: 0.1676 time to fit residues: 103.7020 Evaluate side-chains 291 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 264 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1194 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 1062 LEU Chi-restraints excluded: chain E residue 63 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: [103, 299, 216, 117, 33, 260, 315, 43, 29, 17, 193] chunk 103 optimal weight: 0.7980 chunk 299 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 315 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS C1080 ASN D 266 ASN D 424 ASN D1326 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095283 restraints weight = 51538.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.098536 restraints weight = 24475.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.100578 restraints weight = 15506.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.101776 restraints weight = 11781.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.102569 restraints weight = 10062.180| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26821 Z= 0.153 Angle : 0.691 21.028 36478 Z= 0.349 Chirality : 0.046 0.284 4162 Planarity : 0.005 0.068 4578 Dihedral : 14.193 134.938 4181 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.76 % Favored : 92.18 % Rotamer: Outliers : 2.27 % Allowed : 10.08 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.77 % 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: -2.15 (0.14), residues: 3195 helix: 0.33 (0.15), residues: 1121 sheet: -1.90 (0.25), residues: 394 loop : -2.66 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 293 TYR 0.023 0.001 TYR A 177 PHE 0.014 0.001 PHE C 35 TRP 0.013 0.001 TRP C 183 HIS 0.007 0.001 HIS D 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (26812) covalent geometry : angle 0.67024 / 0.35 (36466) hydrogen bonds : bond 0.05430 / 6.11 ( 1091) hydrogen bonds : angle 5.15315 / 5.18 ( 3019) metal coordination : bond 0.01957 / 2.19 ( 8) metal coordination : angle 9.37520 / 18.04 ( 12) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 283 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.8270 (tttt) cc_final: 0.7922 (tttp) REVERT: A 181 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: A 185 TYR cc_start: 0.9051 (p90) cc_final: 0.8761 (p90) REVERT: B 80 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7437 (mt-10) REVERT: B 186 ASN cc_start: 0.8665 (m-40) cc_final: 0.8337 (m-40) REVERT: B 211 ILE cc_start: 0.8952 (tp) cc_final: 0.8643 (pt) REVERT: C 14 ASP cc_start: 0.8203 (t70) cc_final: 0.7967 (t0) REVERT: C 121 GLU cc_start: 0.7362 (pt0) cc_final: 0.6654 (pp20) REVERT: C 315 MET cc_start: 0.7084 (mtp) cc_final: 0.6843 (mtm) REVERT: C 429 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8418 (mtt) REVERT: C 510 GLN cc_start: 0.8615 (mt0) cc_final: 0.8384 (tt0) REVERT: C 600 THR cc_start: 0.8702 (m) cc_final: 0.8157 (p) REVERT: C 601 ASP cc_start: 0.7949 (p0) cc_final: 0.7709 (p0) REVERT: C 681 MET cc_start: 0.8271 (mtp) cc_final: 0.7999 (mtt) REVERT: C 741 MET cc_start: 0.7750 (tpt) cc_final: 0.7518 (tpt) REVERT: C 979 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.6999 (tp) REVERT: D 111 THR cc_start: 0.9627 (m) cc_final: 0.9409 (p) REVERT: D 129 ASP cc_start: 0.8315 (t70) cc_final: 0.7957 (t70) REVERT: D 201 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8681 (mm) REVERT: D 304 ASP cc_start: 0.7463 (m-30) cc_final: 0.7241 (m-30) REVERT: D 484 MET cc_start: 0.9084 (mtm) cc_final: 0.8817 (mtp) REVERT: D 582 ILE cc_start: 0.8934 (mt) cc_final: 0.8733 (pt) REVERT: D 591 ILE cc_start: 0.9310 (tp) cc_final: 0.8964 (tp) REVERT: D 1048 ARG cc_start: 0.8347 (tpt170) cc_final: 0.7629 (ttp-170) REVERT: D 1208 ASP cc_start: 0.7492 (t0) cc_final: 0.7288 (t0) REVERT: E 8 ASP cc_start: 0.8199 (m-30) cc_final: 0.7223 (m-30) REVERT: E 69 ARG cc_start: 0.7628 (tpp-160) cc_final: 0.7397 (tpp-160) outliers start: 62 outliers final: 28 residues processed: 331 average time/residue: 0.1621 time to fit residues: 86.3091 Evaluate side-chains 283 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 251 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 1062 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: [312, 92, 209, 267, 86, 58, 289, 188, 186, 220, 286] chunk 312 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 209 optimal weight: 5.9990 chunk 267 optimal weight: 0.2980 chunk 86 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 289 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 220 optimal weight: 0.6980 chunk 286 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS D 929 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.115894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.088600 restraints weight = 47992.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.091384 restraints weight = 24677.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.093187 restraints weight = 16082.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.094306 restraints weight = 12323.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.094974 restraints weight = 10524.581| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26821 Z= 0.138 Angle : 0.647 16.063 36478 Z= 0.330 Chirality : 0.045 0.282 4162 Planarity : 0.004 0.071 4578 Dihedral : 13.898 135.086 4179 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.82 % Favored : 93.15 % Rotamer: Outliers : 2.42 % Allowed : 10.96 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.77 % 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: -1.78 (0.14), residues: 3195 helix: 0.66 (0.16), residues: 1123 sheet: -1.76 (0.25), residues: 402 loop : -2.44 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG D 709 TYR 0.020 0.001 TYR A 177 PHE 0.014 0.001 PHE C 35 TRP 0.012 0.001 TRP C 183 HIS 0.005 0.001 HIS D 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (26812) covalent geometry : angle 0.63306 / 0.33 (36466) hydrogen bonds : bond 0.04986 / 5.63 ( 1091) hydrogen bonds : angle 4.93226 / 4.94 ( 3019) metal coordination : bond 0.00780 / 0.76 ( 8) metal coordination : angle 7.35662 / 14.55 ( 12) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 271 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.8380 (tttt) cc_final: 0.8047 (tttp) REVERT: A 181 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: A 185 TYR cc_start: 0.8962 (p90) cc_final: 0.8727 (p90) REVERT: B 80 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7345 (mt-10) REVERT: B 186 ASN cc_start: 0.8621 (m-40) cc_final: 0.8282 (m-40) REVERT: B 211 ILE cc_start: 0.8991 (tp) cc_final: 0.8676 (pt) REVERT: C 600 THR cc_start: 0.8664 (m) cc_final: 0.8188 (p) REVERT: C 601 ASP cc_start: 0.7780 (p0) cc_final: 0.7570 (p0) REVERT: C 768 MET cc_start: 0.8036 (mtp) cc_final: 0.7791 (mtp) REVERT: C 979 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7163 (tp) REVERT: D 129 ASP cc_start: 0.8140 (t70) cc_final: 0.7738 (t70) REVERT: D 142 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7259 (tm-30) REVERT: D 201 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8767 (mm) REVERT: D 453 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8743 (t) REVERT: D 591 ILE cc_start: 0.9264 (tp) cc_final: 0.8958 (tp) REVERT: D 1048 ARG cc_start: 0.8348 (tpt170) cc_final: 0.7799 (ttp-170) REVERT: E 8 ASP cc_start: 0.8005 (m-30) cc_final: 0.7373 (m-30) REVERT: E 69 ARG cc_start: 0.7610 (tpp-160) cc_final: 0.7284 (tpp-160) outliers start: 66 outliers final: 39 residues processed: 319 average time/residue: 0.1583 time to fit residues: 82.3014 Evaluate side-chains 281 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 238 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 638 SER Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 1062 LEU Chi-restraints excluded: chain D residue 1342 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: [159, 4, 209, 2, 168, 196, 312, 208, 202, 143, 146] chunk 159 optimal weight: 0.0980 chunk 4 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 312 optimal weight: 6.9990 chunk 208 optimal weight: 0.8980 chunk 202 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.116864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.089275 restraints weight = 47910.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.092034 restraints weight = 24821.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.093857 restraints weight = 16279.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.094986 restraints weight = 12478.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.095628 restraints weight = 10636.546| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26821 Z= 0.125 Angle : 0.621 12.853 36478 Z= 0.319 Chirality : 0.044 0.272 4162 Planarity : 0.004 0.074 4578 Dihedral : 13.694 136.958 4179 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.60 % Favored : 93.36 % Rotamer: Outliers : 2.31 % Allowed : 12.24 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.15), residues: 3195 helix: 0.89 (0.16), residues: 1122 sheet: -1.59 (0.25), residues: 412 loop : -2.32 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 709 TYR 0.018 0.001 TYR A 177 PHE 0.014 0.001 PHE C 253 TRP 0.012 0.001 TRP C 183 HIS 0.004 0.001 HIS D 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (26812) covalent geometry : angle 0.61165 / 0.32 (36466) hydrogen bonds : bond 0.04747 / 5.35 ( 1091) hydrogen bonds : angle 4.81147 / 4.80 ( 3019) metal coordination : bond 0.00645 / 0.65 ( 8) metal coordination : angle 5.94940 / 11.90 ( 12) Misc. bond : bond 0.00010 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 265 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.8371 (tttt) cc_final: 0.8059 (tttp) REVERT: A 181 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: B 80 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7311 (mt-10) REVERT: B 186 ASN cc_start: 0.8578 (m-40) cc_final: 0.8223 (m-40) REVERT: B 211 ILE cc_start: 0.8990 (tp) cc_final: 0.8701 (pt) REVERT: C 600 THR cc_start: 0.8660 (m) cc_final: 0.8202 (p) REVERT: C 601 ASP cc_start: 0.7755 (p0) cc_final: 0.7527 (p0) REVERT: C 768 MET cc_start: 0.8004 (mtp) cc_final: 0.7742 (mtp) REVERT: C 979 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7039 (tp) REVERT: C 1119 MET cc_start: 0.8420 (tpp) cc_final: 0.8104 (ttt) REVERT: D 129 ASP cc_start: 0.8092 (t70) cc_final: 0.7665 (t70) REVERT: D 142 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7390 (tm-30) REVERT: D 201 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8775 (mm) REVERT: D 304 ASP cc_start: 0.7244 (m-30) cc_final: 0.6990 (m-30) REVERT: D 453 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8771 (t) REVERT: D 591 ILE cc_start: 0.9241 (tp) cc_final: 0.8909 (tp) REVERT: D 802 ASP cc_start: 0.8056 (t0) cc_final: 0.7839 (t0) REVERT: D 1048 ARG cc_start: 0.8278 (tpt170) cc_final: 0.7835 (ttp-170) REVERT: D 1208 ASP cc_start: 0.7256 (t0) cc_final: 0.7008 (t0) REVERT: E 43 ASN cc_start: 0.8468 (m-40) cc_final: 0.7981 (t0) REVERT: E 69 ARG cc_start: 0.7586 (tpp-160) cc_final: 0.7262 (tpp-160) outliers start: 63 outliers final: 39 residues processed: 309 average time/residue: 0.1530 time to fit residues: 77.3527 Evaluate side-chains 284 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 241 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 1062 LEU Chi-restraints excluded: chain D residue 1342 ASP Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: [229, 283, 55, 179, 116, 255, 81, 156, 215, 248, 176] chunk 229 optimal weight: 0.9990 chunk 283 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 116 optimal weight: 0.0470 chunk 255 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 248 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 overall best weight: 1.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.116777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.089390 restraints weight = 47884.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.092163 restraints weight = 24691.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.093970 restraints weight = 16128.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.095101 restraints weight = 12355.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.095694 restraints weight = 10513.051| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26821 Z= 0.133 Angle : 0.620 10.311 36478 Z= 0.317 Chirality : 0.044 0.252 4162 Planarity : 0.004 0.072 4578 Dihedral : 13.566 137.904 4179 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.76 % Favored : 93.21 % Rotamer: Outliers : 2.09 % Allowed : 13.34 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.15), residues: 3195 helix: 1.03 (0.16), residues: 1123 sheet: -1.54 (0.24), residues: 424 loop : -2.21 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 293 TYR 0.027 0.001 TYR A 185 PHE 0.012 0.001 PHE D 176 TRP 0.012 0.001 TRP C 183 HIS 0.004 0.001 HIS D 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (26812) covalent geometry : angle 0.61282 / 0.32 (36466) hydrogen bonds : bond 0.04648 / 5.24 ( 1091) hydrogen bonds : angle 4.71933 / 4.72 ( 3019) metal coordination : bond 0.00600 / 0.62 ( 8) metal coordination : angle 5.07410 / 10.16 ( 12) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 259 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.8409 (tttt) cc_final: 0.8096 (tttp) REVERT: A 181 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: B 80 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7316 (mt-10) REVERT: B 186 ASN cc_start: 0.8581 (m-40) cc_final: 0.8228 (m-40) REVERT: B 211 ILE cc_start: 0.9004 (tp) cc_final: 0.8726 (pt) REVERT: C 272 ARG cc_start: 0.5890 (mtt180) cc_final: 0.5612 (tmm-80) REVERT: C 600 THR cc_start: 0.8650 (m) cc_final: 0.8212 (p) REVERT: C 601 ASP cc_start: 0.7746 (p0) cc_final: 0.7525 (p0) REVERT: C 768 MET cc_start: 0.7985 (mtp) cc_final: 0.7735 (mtp) REVERT: C 979 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7088 (tp) REVERT: C 1119 MET cc_start: 0.8366 (tpp) cc_final: 0.8143 (ttt) REVERT: D 129 ASP cc_start: 0.8012 (t70) cc_final: 0.7642 (t70) REVERT: D 142 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7243 (tm-30) REVERT: D 201 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8758 (mm) REVERT: D 453 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8756 (t) REVERT: D 568 SER cc_start: 0.8579 (t) cc_final: 0.8361 (p) REVERT: D 591 ILE cc_start: 0.9280 (tp) cc_final: 0.8940 (tp) REVERT: D 1048 ARG cc_start: 0.8306 (tpt170) cc_final: 0.7818 (ttp-170) REVERT: D 1208 ASP cc_start: 0.7407 (t0) cc_final: 0.7102 (t0) REVERT: D 1334 GLU cc_start: 0.7536 (tp30) cc_final: 0.7301 (tp30) REVERT: E 8 ASP cc_start: 0.8283 (m-30) cc_final: 0.7402 (m-30) REVERT: E 11 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: E 43 ASN cc_start: 0.8466 (m-40) cc_final: 0.7997 (t0) REVERT: E 56 GLU cc_start: 0.8498 (tp30) cc_final: 0.8288 (tp30) REVERT: E 69 ARG cc_start: 0.7635 (tpp-160) cc_final: 0.7321 (tpp-160) outliers start: 57 outliers final: 38 residues processed: 301 average time/residue: 0.1572 time to fit residues: 76.6150 Evaluate side-chains 282 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 239 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 1062 LEU Chi-restraints excluded: chain D residue 1342 ASP Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: [221, 196, 69, 122, 262, 201, 147, 107, 40, 142, 144] chunk 221 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 262 optimal weight: 1.9990 chunk 201 optimal weight: 0.5980 chunk 147 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 40 optimal weight: 0.0670 chunk 142 optimal weight: 0.5980 chunk 144 optimal weight: 6.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.117828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.090126 restraints weight = 47822.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.092941 restraints weight = 24836.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.094732 restraints weight = 16255.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095912 restraints weight = 12529.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.096602 restraints weight = 10657.993| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26821 Z= 0.118 Angle : 0.596 7.680 36478 Z= 0.307 Chirality : 0.043 0.222 4162 Planarity : 0.004 0.073 4578 Dihedral : 13.420 139.386 4179 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.10 % Favored : 93.87 % Rotamer: Outliers : 1.87 % Allowed : 13.82 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.15), residues: 3195 helix: 1.17 (0.16), residues: 1128 sheet: -1.44 (0.24), residues: 428 loop : -2.12 (0.14), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 706 TYR 0.026 0.001 TYR A 185 PHE 0.011 0.001 PHE D 176 TRP 0.011 0.001 TRP C 183 HIS 0.003 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (26812) covalent geometry : angle 0.59143 / 0.31 (36466) hydrogen bonds : bond 0.04419 / 5.00 ( 1091) hydrogen bonds : angle 4.59884 / 4.59 ( 3019) metal coordination : bond 0.00456 / 0.46 ( 8) metal coordination : angle 4.02762 / 8.12 ( 12) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 265 time to evaluate : 1.681 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.8377 (tttt) cc_final: 0.8064 (tttp) REVERT: B 80 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7287 (mt-10) REVERT: B 145 LYS cc_start: 0.8813 (ttpt) cc_final: 0.8395 (ptpt) REVERT: B 211 ILE cc_start: 0.9006 (tp) cc_final: 0.8745 (pt) REVERT: C 272 ARG cc_start: 0.5840 (mtt180) cc_final: 0.5593 (tmm-80) REVERT: C 459 MET cc_start: 0.8667 (mtm) cc_final: 0.8338 (mtp) REVERT: C 600 THR cc_start: 0.8603 (m) cc_final: 0.8155 (p) REVERT: C 601 ASP cc_start: 0.7723 (p0) cc_final: 0.7518 (p0) REVERT: C 768 MET cc_start: 0.7993 (mtp) cc_final: 0.7672 (mtp) REVERT: C 785 ASP cc_start: 0.8292 (m-30) cc_final: 0.8080 (m-30) REVERT: C 979 LEU cc_start: 0.7373 (mt) cc_final: 0.7087 (tp) REVERT: C 1119 MET cc_start: 0.8350 (tpp) cc_final: 0.8095 (ttt) REVERT: C 1329 GLU cc_start: 0.7662 (mt-10) cc_final: 0.6908 (mt-10) REVERT: D 129 ASP cc_start: 0.8030 (t70) cc_final: 0.7664 (t70) REVERT: D 142 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7331 (tm-30) REVERT: D 201 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8750 (mm) REVERT: D 304 ASP cc_start: 0.7342 (m-30) cc_final: 0.7114 (m-30) REVERT: D 453 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8755 (t) REVERT: D 568 SER cc_start: 0.8539 (t) cc_final: 0.8313 (p) REVERT: D 1048 ARG cc_start: 0.8277 (tpt170) cc_final: 0.7784 (ttp-170) REVERT: D 1208 ASP cc_start: 0.7420 (t0) cc_final: 0.7080 (t0) REVERT: D 1334 GLU cc_start: 0.7508 (tp30) cc_final: 0.7287 (tp30) REVERT: E 43 ASN cc_start: 0.8467 (m-40) cc_final: 0.8064 (t0) REVERT: E 49 ILE cc_start: 0.8864 (tp) cc_final: 0.8637 (tp) REVERT: E 69 ARG cc_start: 0.7614 (tpp-160) cc_final: 0.7277 (tpp-160) outliers start: 51 outliers final: 37 residues processed: 306 average time/residue: 0.1565 time to fit residues: 77.9152 Evaluate side-chains 278 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 1062 LEU Chi-restraints excluded: chain D residue 1342 ASP Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: [177, 229, 52, 71, 128, 273, 285, 263, 236, 207, 102] chunk 177 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 273 optimal weight: 0.7980 chunk 285 optimal weight: 0.1980 chunk 263 optimal weight: 3.9990 chunk 236 optimal weight: 0.6980 chunk 207 optimal weight: 4.9990 chunk 102 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS D1244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.118304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.090800 restraints weight = 47737.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.094072 restraints weight = 24741.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.095682 restraints weight = 15056.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.096024 restraints weight = 11469.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096201 restraints weight = 11609.250| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26821 Z= 0.110 Angle : 0.596 12.948 36478 Z= 0.306 Chirality : 0.043 0.223 4162 Planarity : 0.004 0.073 4578 Dihedral : 13.339 140.101 4179 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.07 % Favored : 93.90 % Rotamer: Outliers : 1.87 % Allowed : 14.48 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.15), residues: 3195 helix: 1.31 (0.16), residues: 1121 sheet: -1.32 (0.25), residues: 427 loop : -2.03 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 137 TYR 0.024 0.001 TYR A 185 PHE 0.007 0.001 PHE C 828 TRP 0.010 0.001 TRP C 183 HIS 0.004 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (26812) covalent geometry : angle 0.59231 / 0.31 (36466) hydrogen bonds : bond 0.04282 / 4.84 ( 1091) hydrogen bonds : angle 4.53200 / 4.53 ( 3019) metal coordination : bond 0.00382 / 0.38 ( 8) metal coordination : angle 3.70182 / 7.41 ( 12) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 251 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.8416 (tttt) cc_final: 0.8144 (tttp) REVERT: A 181 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: B 145 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8431 (ptmm) REVERT: B 211 ILE cc_start: 0.9011 (tp) cc_final: 0.8780 (pt) REVERT: C 272 ARG cc_start: 0.5834 (mtt180) cc_final: 0.5614 (tmm-80) REVERT: C 459 MET cc_start: 0.8642 (mtm) cc_final: 0.8341 (mtp) REVERT: C 600 THR cc_start: 0.8536 (m) cc_final: 0.8124 (p) REVERT: C 601 ASP cc_start: 0.7630 (p0) cc_final: 0.7427 (p0) REVERT: C 979 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7091 (tp) REVERT: D 129 ASP cc_start: 0.7899 (t70) cc_final: 0.7537 (t70) REVERT: D 142 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7208 (tm-30) REVERT: D 201 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8724 (mm) REVERT: D 300 GLN cc_start: 0.8298 (tp40) cc_final: 0.7588 (tm-30) REVERT: D 304 ASP cc_start: 0.7374 (m-30) cc_final: 0.6126 (m-30) REVERT: D 453 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8697 (t) REVERT: D 1048 ARG cc_start: 0.8257 (tpt170) cc_final: 0.7772 (ttp-170) REVERT: D 1208 ASP cc_start: 0.7378 (t0) cc_final: 0.7029 (t0) REVERT: D 1334 GLU cc_start: 0.7378 (tp30) cc_final: 0.7176 (tp30) REVERT: E 8 ASP cc_start: 0.8117 (m-30) cc_final: 0.7897 (m-30) REVERT: E 43 ASN cc_start: 0.8380 (m-40) cc_final: 0.8010 (t0) REVERT: E 49 ILE cc_start: 0.8869 (tp) cc_final: 0.8618 (tp) REVERT: E 69 ARG cc_start: 0.7658 (tpp-160) cc_final: 0.7341 (tpp-160) outliers start: 51 outliers final: 38 residues processed: 291 average time/residue: 0.1580 time to fit residues: 75.0804 Evaluate side-chains 272 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 1062 LEU Chi-restraints excluded: chain D residue 1342 ASP Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: [187, 279, 120, 237, 131, 294, 222, 128, 147, 143, 118] chunk 187 optimal weight: 2.9990 chunk 279 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 237 optimal weight: 0.4980 chunk 131 optimal weight: 0.0870 chunk 294 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 143 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN D 424 ASN D 921 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.118062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.090868 restraints weight = 47831.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.094252 restraints weight = 24725.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.095158 restraints weight = 15139.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.095494 restraints weight = 12130.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.095804 restraints weight = 12162.368| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26821 Z= 0.126 Angle : 0.608 11.650 36478 Z= 0.312 Chirality : 0.043 0.225 4162 Planarity : 0.004 0.072 4578 Dihedral : 13.284 140.558 4179 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.92 % Favored : 94.05 % Rotamer: Outliers : 1.91 % Allowed : 14.66 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.15), residues: 3195 helix: 1.38 (0.16), residues: 1120 sheet: -1.21 (0.24), residues: 443 loop : -2.00 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1058 TYR 0.021 0.001 TYR B 185 PHE 0.011 0.001 PHE D 620 TRP 0.011 0.001 TRP C 183 HIS 0.005 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (26812) covalent geometry : angle 0.60419 / 0.31 (36466) hydrogen bonds : bond 0.04301 / 4.86 ( 1091) hydrogen bonds : angle 4.51417 / 4.52 ( 3019) metal coordination : bond 0.00467 / 0.49 ( 8) metal coordination : angle 3.64514 / 7.23 ( 12) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 249 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.8519 (tttt) cc_final: 0.8220 (tttp) REVERT: A 181 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: B 145 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8443 (ptmm) REVERT: B 200 LYS cc_start: 0.9275 (tttt) cc_final: 0.9054 (ttpp) REVERT: B 211 ILE cc_start: 0.9034 (tp) cc_final: 0.8785 (pt) REVERT: C 272 ARG cc_start: 0.5819 (mtt180) cc_final: 0.5536 (tmm-80) REVERT: C 459 MET cc_start: 0.8648 (mtm) cc_final: 0.8375 (mtp) REVERT: C 600 THR cc_start: 0.8538 (m) cc_final: 0.8112 (p) REVERT: C 979 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.7047 (tp) REVERT: C 1329 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7305 (mt-10) REVERT: D 129 ASP cc_start: 0.7845 (t70) cc_final: 0.7489 (t70) REVERT: D 201 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8735 (mm) REVERT: D 300 GLN cc_start: 0.8364 (tp40) cc_final: 0.7601 (tm-30) REVERT: D 304 ASP cc_start: 0.7375 (m-30) cc_final: 0.6111 (m-30) REVERT: D 453 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8744 (t) REVERT: D 1048 ARG cc_start: 0.8263 (tpt170) cc_final: 0.7833 (ttt180) REVERT: D 1208 ASP cc_start: 0.7428 (t0) cc_final: 0.7060 (t0) REVERT: E 8 ASP cc_start: 0.8121 (m-30) cc_final: 0.7606 (m-30) REVERT: E 43 ASN cc_start: 0.8399 (m-40) cc_final: 0.8032 (t0) REVERT: E 49 ILE cc_start: 0.8868 (tp) cc_final: 0.8633 (tp) REVERT: E 69 ARG cc_start: 0.7705 (tpp-160) cc_final: 0.7401 (tpp-160) outliers start: 52 outliers final: 41 residues processed: 291 average time/residue: 0.1633 time to fit residues: 77.0853 Evaluate side-chains 283 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 238 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 1062 LEU Chi-restraints excluded: chain D residue 1342 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: [201, 74, 128, 136, 212, 205, 29, 313, 163, 241, 181] chunk 201 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 212 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 313 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 241 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.116601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.089433 restraints weight = 47784.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.092560 restraints weight = 25189.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.093237 restraints weight = 15497.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.094125 restraints weight = 13509.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.094166 restraints weight = 11465.639| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26821 Z= 0.165 Angle : 0.636 11.716 36478 Z= 0.325 Chirality : 0.044 0.324 4162 Planarity : 0.004 0.072 4578 Dihedral : 13.276 140.805 4179 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.51 % Favored : 93.46 % Rotamer: Outliers : 1.69 % Allowed : 15.18 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.15), residues: 3195 helix: 1.35 (0.16), residues: 1120 sheet: -1.24 (0.24), residues: 452 loop : -2.00 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 211 TYR 0.023 0.001 TYR A 185 PHE 0.012 0.001 PHE D 620 TRP 0.013 0.001 TRP C 183 HIS 0.004 0.001 HIS D 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (26812) covalent geometry : angle 0.63220 / 0.32 (36466) hydrogen bonds : bond 0.04510 / 5.07 ( 1091) hydrogen bonds : angle 4.53790 / 4.62 ( 3019) metal coordination : bond 0.00699 / 0.74 ( 8) metal coordination : angle 3.76038 / 7.44 ( 12) Misc. bond : bond 0.00003 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.8563 (tttt) cc_final: 0.8258 (tttp) REVERT: A 181 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: B 145 LYS cc_start: 0.8784 (ttpt) cc_final: 0.8460 (ptmm) REVERT: B 200 LYS cc_start: 0.9272 (tttt) cc_final: 0.9044 (ttpp) REVERT: B 211 ILE cc_start: 0.9053 (tp) cc_final: 0.8794 (pt) REVERT: C 65 ASN cc_start: 0.6327 (m-40) cc_final: 0.6048 (m-40) REVERT: C 272 ARG cc_start: 0.5828 (mtt180) cc_final: 0.5536 (tmm-80) REVERT: C 600 THR cc_start: 0.8519 (m) cc_final: 0.8116 (p) REVERT: C 979 LEU cc_start: 0.7362 (mt) cc_final: 0.7087 (tp) REVERT: D 129 ASP cc_start: 0.7852 (t70) cc_final: 0.7492 (t70) REVERT: D 142 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7147 (tm-30) REVERT: D 201 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8733 (mm) REVERT: D 298 MET cc_start: 0.8556 (tpp) cc_final: 0.8316 (mmt) REVERT: D 453 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8780 (t) REVERT: D 1048 ARG cc_start: 0.8226 (tpt170) cc_final: 0.7858 (ttt180) REVERT: D 1208 ASP cc_start: 0.7436 (t0) cc_final: 0.7098 (t0) REVERT: E 43 ASN cc_start: 0.8408 (m-40) cc_final: 0.8031 (t0) REVERT: E 49 ILE cc_start: 0.8889 (tp) cc_final: 0.8636 (tp) REVERT: E 69 ARG cc_start: 0.7668 (tpp-160) cc_final: 0.7351 (tpp-160) outliers start: 46 outliers final: 39 residues processed: 274 average time/residue: 0.1614 time to fit residues: 71.7223 Evaluate side-chains 272 residues out of total 2728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 1062 LEU Chi-restraints excluded: chain D residue 1342 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: [105, 93, 181, 236, 258, 310, 274, 251, 232, 265, 211] chunk 105 optimal weight: 0.0050 chunk 93 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 chunk 236 optimal weight: 0.9990 chunk 258 optimal weight: 0.9980 chunk 310 optimal weight: 2.9990 chunk 274 optimal weight: 0.7980 chunk 251 optimal weight: 0.8980 chunk 232 optimal weight: 2.9990 chunk 265 optimal weight: 0.0870 chunk 211 optimal weight: 0.8980 overall best weight: 0.5372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.119108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.091516 restraints weight = 47349.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.094333 restraints weight = 24559.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.096128 restraints weight = 16058.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.097257 restraints weight = 12368.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.097981 restraints weight = 10557.912| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26821 Z= 0.111 Angle : 0.602 11.839 36478 Z= 0.310 Chirality : 0.043 0.231 4162 Planarity : 0.004 0.071 4578 Dihedral : 13.146 142.012 4179 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.83 % Allowed : 15.14 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.15), residues: 3195 helix: 1.41 (0.16), residues: 1124 sheet: -1.07 (0.25), residues: 434 loop : -1.95 (0.14), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.026 0.001 TYR A 185 PHE 0.012 0.001 PHE C1025 TRP 0.009 0.001 TRP C 183 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (26812) covalent geometry : angle 0.59969 / 0.31 (36466) hydrogen bonds : bond 0.04168 / 4.74 ( 1091) hydrogen bonds : angle 4.45481 / 4.50 ( 3019) metal coordination : bond 0.00310 / 0.31 ( 8) metal coordination : angle 3.02880 / 6.01 ( 12) Misc. bond : bond 0.00014 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3945.11 seconds wall clock time: 68 minutes 54.90 seconds (4134.90 seconds total)