Starting phenix.real_space_refine on Sat Jul 4 02:25:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q9i_52960/07_2026/9q9i_52960.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q9i_52960/07_2026/9q9i_52960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q9i_52960/07_2026/9q9i_52960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q9i_52960/07_2026/9q9i_52960.map" model { file = "/net/cci-nas-00/data/ceres_data/9q9i_52960/07_2026/9q9i_52960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q9i_52960/07_2026/9q9i_52960.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.065 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: 9 Type Number sf(0) Gaussians Mn 2 7.51 5 P 58 5.49 5 Mg 2 5.21 5 S 80 5.16 5 Be 2 3.05 5 C 10649 2.51 5 N 2981 2.21 5 O 3341 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17121 Number of models: 1 Model: "" Number of chains: 13 Chain: "P" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 540 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "T" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 567 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 703 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain breaks: 1 Chain: "A" Number of atoms: 3791 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 468, 3783 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 459} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 468, 3783 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 459} Chain breaks: 1 bond proxies already assigned to first conformer: 3824 Chain: "B" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3777 Classifications: {'peptide': 467} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 458} Chain breaks: 2 Chain: "D" Number of atoms: 3805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3805 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 20, 'TRANS': 446} Chain breaks: 2 Chain: "E" Number of atoms: 3868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3868 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 20, 'TRANS': 453} Chain breaks: 2 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.52, per 1000 atoms: 0.26 Number of scatterers: 17121 At special positions: 0 Unit cell: (98.145, 109.777, 181.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Mn 2 24.99 S 80 16.00 P 58 15.00 Mg 2 11.99 F 6 9.00 O 3341 8.00 N 2981 7.00 C 10649 6.00 Be 2 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 831.5 milliseconds 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3732 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 20 sheets defined 45.1% alpha, 16.6% beta 26 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'F' and resid 716 through 746 Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 41 through 55 removed outlier: 3.851A pdb=" N ILE A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.802A pdb=" N VAL A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.869A pdb=" N ARG A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 182 through 236 removed outlier: 3.584A pdb=" N ILE A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1093 Processing helix chain 'A' and resid 1094 through 1099 removed outlier: 3.518A pdb=" N ASP A1099 " --> pdb=" O PRO A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1140 Processing helix chain 'A' and resid 1140 through 1155 removed outlier: 3.791A pdb=" N ASP A1149 " --> pdb=" O LYS A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1221 Processing helix chain 'A' and resid 1238 through 1257 Processing helix chain 'A' and resid 1270 through 1279 Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.755A pdb=" N LYS B 22 " --> pdb=" O ASP B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 55 removed outlier: 3.662A pdb=" N ILE B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 145 Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 182 through 237 removed outlier: 3.755A pdb=" N ILE B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS B 211 " --> pdb=" O GLN B 207 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR B 212 " --> pdb=" O MET B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1094 removed outlier: 4.065A pdb=" N ILE B1085 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B1086 " --> pdb=" O GLU B1082 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1099 removed outlier: 3.883A pdb=" N ASP B1099 " --> pdb=" O PRO B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1155 removed outlier: 4.277A pdb=" N GLU B1142 " --> pdb=" O MET B1138 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE B1143 " --> pdb=" O LYS B1139 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B1145 " --> pdb=" O GLU B1141 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE B1146 " --> pdb=" O GLU B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1222 Processing helix chain 'B' and resid 1238 through 1257 Processing helix chain 'B' and resid 1270 through 1277 Processing helix chain 'B' and resid 1305 through 1310 removed outlier: 4.910A pdb=" N GLY B1308 " --> pdb=" O SER B1305 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE B1309 " --> pdb=" O SER B1306 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 51 Processing helix chain 'D' and resid 68 through 83 Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 109 through 113 Processing helix chain 'D' and resid 127 through 131 removed outlier: 3.784A pdb=" N ASP D 131 " --> pdb=" O ASN D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 148 Processing helix chain 'D' and resid 185 through 195 Processing helix chain 'D' and resid 206 through 210 removed outlier: 4.237A pdb=" N TRP D 210 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 234 Processing helix chain 'D' and resid 315 through 317 No H-bonds generated for 'chain 'D' and resid 315 through 317' Processing helix chain 'D' and resid 327 through 351 removed outlier: 3.827A pdb=" N ALA D 331 " --> pdb=" O LYS D 327 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN D 333 " --> pdb=" O THR D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 383 Processing helix chain 'D' and resid 429 through 444 Processing helix chain 'D' and resid 453 through 464 Processing helix chain 'D' and resid 468 through 488 removed outlier: 3.765A pdb=" N LEU D 473 " --> pdb=" O ALA D 469 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D 488 " --> pdb=" O PHE D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 504 removed outlier: 3.837A pdb=" N ASP D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 50 Processing helix chain 'E' and resid 68 through 83 Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.552A pdb=" N ASN E 100 " --> pdb=" O ASP E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 139 through 148 Processing helix chain 'E' and resid 185 through 195 Processing helix chain 'E' and resid 206 through 210 removed outlier: 3.781A pdb=" N TRP E 210 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 280 removed outlier: 3.595A pdb=" N ALA E 279 " --> pdb=" O PRO E 276 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL E 280 " --> pdb=" O GLY E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 317 No H-bonds generated for 'chain 'E' and resid 315 through 317' Processing helix chain 'E' and resid 327 through 351 removed outlier: 3.659A pdb=" N ALA E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 382 Processing helix chain 'E' and resid 383 through 386 removed outlier: 4.148A pdb=" N VAL E 386 " --> pdb=" O GLN E 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 383 through 386' Processing helix chain 'E' and resid 428 through 442 removed outlier: 3.645A pdb=" N LEU E 432 " --> pdb=" O ARG E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 465 Processing helix chain 'E' and resid 468 through 488 Processing helix chain 'E' and resid 493 through 507 Processing sheet with id=AA1, first strand: chain 'F' and resid 656 through 660 removed outlier: 3.919A pdb=" N LEU F 656 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU F 658 " --> pdb=" O MET D 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 708 through 710 removed outlier: 3.756A pdb=" N LEU E 201 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 26 removed outlier: 6.790A pdb=" N GLN A 85 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET A 7 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG A 83 " --> pdb=" O MET A 7 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE A 9 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN A 81 " --> pdb=" O ILE A 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 23 through 26 removed outlier: 6.790A pdb=" N GLN A 85 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET A 7 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG A 83 " --> pdb=" O MET A 7 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE A 9 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN A 81 " --> pdb=" O ILE A 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1226 through 1231 removed outlier: 7.096A pdb=" N GLY A1226 " --> pdb=" O GLN A1263 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU A1265 " --> pdb=" O GLY A1226 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE A1228 " --> pdb=" O LEU A1265 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE A1267 " --> pdb=" O ILE A1228 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A1230 " --> pdb=" O ILE A1267 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N THR A 32 " --> pdb=" O VAL A1266 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N LEU A 31 " --> pdb=" O LYS A1285 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N TYR A1287 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE A 33 " --> pdb=" O TYR A1287 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ILE A1289 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 35 " --> pdb=" O ILE A1289 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N LYS A1291 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A1300 " --> pdb=" O ARG A1288 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA7, first strand: chain 'A' and resid 1163 through 1168 removed outlier: 4.129A pdb=" N ASN A1183 " --> pdb=" O ASP A1168 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR A1193 " --> pdb=" O LYS A1190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 23 through 26 removed outlier: 6.529A pdb=" N GLN B 85 " --> pdb=" O GLU B 5 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N MET B 7 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG B 83 " --> pdb=" O MET B 7 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE B 9 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLN B 81 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER B 99 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 23 through 26 removed outlier: 6.529A pdb=" N GLN B 85 " --> pdb=" O GLU B 5 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N MET B 7 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG B 83 " --> pdb=" O MET B 7 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE B 9 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLN B 81 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1230 through 1231 removed outlier: 6.772A pdb=" N LEU B1230 " --> pdb=" O ILE B1267 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE B 33 " --> pdb=" O TYR B1287 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE B1289 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 35 " --> pdb=" O ILE B1289 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N LYS B1291 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.859A pdb=" N LYS B 105 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1164 through 1167 removed outlier: 4.102A pdb=" N THR B1193 " --> pdb=" O LYS B1190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 151 through 152 removed outlier: 6.692A pdb=" N VAL D 122 " --> pdb=" O ASN D 151 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE D 55 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU D 16 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY D 285 " --> pdb=" O VAL D 17 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 92 through 93 removed outlier: 3.582A pdb=" N GLN D 170 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS D 175 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU D 213 " --> pdb=" O LYS D 175 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA D 177 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL D 215 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYR D 179 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASN D 212 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE D 242 " --> pdb=" O ASN D 212 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE D 214 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL D 241 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE D 263 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA D 252 " --> pdb=" O ILE D 263 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 307 through 313 Processing sheet with id=AB7, first strand: chain 'E' and resid 15 through 16 removed outlier: 6.144A pdb=" N ILE E 55 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL E 122 " --> pdb=" O ASN E 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 167 through 171 removed outlier: 4.124A pdb=" N HIS E 217 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE E 214 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N GLY E 244 " --> pdb=" O PHE E 214 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE E 216 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL E 241 " --> pdb=" O SER E 264 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE E 263 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA E 252 " --> pdb=" O ILE E 263 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 283 through 284 Processing sheet with id=AC1, first strand: chain 'E' and resid 287 through 290 removed outlier: 3.669A pdb=" N LYS E 293 " --> pdb=" O LYS E 290 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 307 through 313 removed outlier: 6.689A pdb=" N PHE E 308 " --> pdb=" O ARG E 364 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ARG E 366 " --> pdb=" O PHE E 308 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU E 310 " --> pdb=" O ARG E 366 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASP E 368 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE E 312 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE E 399 " --> pdb=" O VAL E 367 " (cutoff:3.500A) 771 hydrogen bonds defined for protein. 2193 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 3.75 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2836 1.31 - 1.44: 4615 1.44 - 1.56: 9833 1.56 - 1.69: 112 1.69 - 1.81: 126 Bond restraints: 17522 Sorted by residual: bond pdb=" C4 ADP B1402 " pdb=" C5 ADP B1402 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C4 ADP A1402 " pdb=" C5 ADP A1402 " ideal model delta sigma weight residual 1.490 1.377 0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C MET D 84 " pdb=" N GLY D 85 " ideal model delta sigma weight residual 1.327 1.276 0.051 9.60e-03 1.09e+04 2.83e+01 bond pdb=" C GLU E 466 " pdb=" N LYS E 467 " ideal model delta sigma weight residual 1.331 1.402 -0.072 1.40e-02 5.10e+03 2.61e+01 bond pdb=" C3' DA T 26 " pdb=" O3' DA T 26 " ideal model delta sigma weight residual 1.435 1.501 -0.066 1.30e-02 5.92e+03 2.57e+01 ... (remaining 17517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 23531 3.79 - 7.58: 240 7.58 - 11.37: 27 11.37 - 15.16: 3 15.16 - 18.94: 3 Bond angle restraints: 23804 Sorted by residual: angle pdb=" N GLU A 135 " pdb=" CA GLU A 135 " pdb=" C GLU A 135 " ideal model delta sigma weight residual 113.97 103.41 10.56 1.28e+00 6.10e-01 6.80e+01 angle pdb=" C ARG F 714 " pdb=" CA ARG F 714 " pdb=" CB ARG F 714 " ideal model delta sigma weight residual 116.54 108.57 7.97 1.15e+00 7.56e-01 4.80e+01 angle pdb=" N ILE A1143 " pdb=" CA ILE A1143 " pdb=" C ILE A1143 " ideal model delta sigma weight residual 111.45 105.31 6.14 9.30e-01 1.16e+00 4.36e+01 angle pdb=" N MET A1140 " pdb=" CA MET A1140 " pdb=" C MET A1140 " ideal model delta sigma weight residual 113.17 105.06 8.11 1.26e+00 6.30e-01 4.14e+01 angle pdb=" CA PHE D 228 " pdb=" CB PHE D 228 " pdb=" CG PHE D 228 " ideal model delta sigma weight residual 113.80 120.21 -6.41 1.00e+00 1.00e+00 4.10e+01 ... (remaining 23799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.47: 9904 34.47 - 68.93: 720 68.93 - 103.40: 23 103.40 - 137.86: 0 137.86 - 172.33: 1 Dihedral angle restraints: 10648 sinusoidal: 4918 harmonic: 5730 Sorted by residual: dihedral pdb=" CD ARG D 488 " pdb=" NE ARG D 488 " pdb=" CZ ARG D 488 " pdb=" NH1 ARG D 488 " ideal model delta sinusoidal sigma weight residual 0.00 -59.66 59.66 1 1.00e+01 1.00e-02 4.75e+01 dihedral pdb=" CD ARG E 452 " pdb=" NE ARG E 452 " pdb=" CZ ARG E 452 " pdb=" NH1 ARG E 452 " ideal model delta sinusoidal sigma weight residual 0.00 41.48 -41.48 1 1.00e+01 1.00e-02 2.41e+01 dihedral pdb=" CD ARG D 452 " pdb=" NE ARG D 452 " pdb=" CZ ARG D 452 " pdb=" NH1 ARG D 452 " ideal model delta sinusoidal sigma weight residual 0.00 -38.43 38.43 1 1.00e+01 1.00e-02 2.08e+01 ... (remaining 10645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 2559 0.143 - 0.286: 63 0.286 - 0.429: 1 0.429 - 0.572: 11 0.572 - 0.715: 1 Chirality restraints: 2635 Sorted by residual: chirality pdb=" P DT P 28 " pdb=" OP1 DT P 28 " pdb=" OP2 DT P 28 " pdb=" O5' DT P 28 " both_signs ideal model delta sigma weight residual True 2.34 -3.05 -0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" P DA T 32 " pdb=" OP1 DA T 32 " pdb=" OP2 DA T 32 " pdb=" O5' DA T 32 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.57 2.00e-01 2.50e+01 8.08e+00 chirality pdb=" P DT P 5 " pdb=" OP1 DT P 5 " pdb=" OP2 DT P 5 " pdb=" O5' DT P 5 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.56 2.00e-01 2.50e+01 7.76e+00 ... (remaining 2632 not shown) Planarity restraints: 2881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 488 " 0.941 9.50e-02 1.11e+02 4.22e-01 1.08e+02 pdb=" NE ARG D 488 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG D 488 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 488 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D 488 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 452 " -0.722 9.50e-02 1.11e+02 3.23e-01 6.37e+01 pdb=" NE ARG E 452 " 0.043 2.00e-02 2.50e+03 pdb=" CZ ARG E 452 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG E 452 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 452 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 452 " 0.658 9.50e-02 1.11e+02 2.95e-01 5.32e+01 pdb=" NE ARG D 452 " -0.041 2.00e-02 2.50e+03 pdb=" CZ ARG D 452 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG D 452 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 452 " 0.019 2.00e-02 2.50e+03 ... (remaining 2878 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 26 2.44 - 3.06: 10868 3.06 - 3.67: 26111 3.67 - 4.29: 39910 4.29 - 4.90: 65560 Nonbonded interactions: 142475 Sorted by model distance: nonbonded pdb=" ND1 HIS E 245 " pdb="MN MN E 801 " model vdw 1.829 3.140 nonbonded pdb="MG MG A1401 " pdb=" O2B ADP A1402 " model vdw 1.884 2.170 nonbonded pdb="MG MG B1401 " pdb=" O2B ADP B1402 " model vdw 1.924 2.170 nonbonded pdb=" OG1 THR A 43 " pdb="MG MG A1401 " model vdw 1.984 2.170 nonbonded pdb="MG MG B1401 " pdb=" O HOH B1501 " model vdw 1.996 2.170 ... (remaining 142470 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 2 through 78 or resid 80 through 120 or resid 125 through \ 1309)) selection = (chain 'B' and (resid 2 through 78 or resid 80 through 236 or resid 1078 through \ 1309)) } ncs_group { reference = (chain 'D' and (resid 8 through 221 or resid 227 through 801)) selection = (chain 'E' and (resid 8 through 221 or resid 227 through 402 or resid 429 throug \ h 504 or resid 801)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 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: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.540 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 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 : 0.006 0.114 17522 Z= 0.393 Angle : 0.969 18.944 23804 Z= 0.617 Chirality : 0.065 0.715 2635 Planarity : 0.017 0.422 2881 Dihedral : 20.291 172.327 6916 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.80 % Allowed : 28.72 % Favored : 69.48 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.19), residues: 1935 helix: 1.45 (0.18), residues: 797 sheet: -0.62 (0.27), residues: 376 loop : -1.23 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 452 TYR 0.013 0.001 TYR B 185 PHE 0.032 0.001 PHE D 228 TRP 0.007 0.001 TRP A 164 HIS 0.010 0.001 HIS B 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.39 (17522) covalent geometry : angle 0.96875 / 0.62 (23804) hydrogen bonds : bond 0.15786 / 16.73 ( 801) hydrogen bonds : angle 6.93629 / 7.60 ( 2297) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 711 HIS cc_start: 0.5774 (OUTLIER) cc_final: 0.5322 (t70) REVERT: A 62 LYS cc_start: 0.6669 (mmtt) cc_final: 0.5891 (mttp) REVERT: A 75 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7316 (mm-30) REVERT: A 92 GLU cc_start: 0.6819 (mp0) cc_final: 0.6434 (mp0) REVERT: A 132 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8045 (ttmm) REVERT: A 133 CYS cc_start: 0.8241 (m) cc_final: 0.7606 (t) REVERT: A 178 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7232 (pt0) REVERT: A 202 LYS cc_start: 0.7635 (mttt) cc_final: 0.7358 (mtmt) REVERT: A 208 MET cc_start: 0.8533 (tpp) cc_final: 0.7692 (tmt) REVERT: A 1107 MET cc_start: 0.7001 (mmm) cc_final: 0.6466 (tpp) REVERT: A 1108 MET cc_start: 0.7607 (tpp) cc_final: 0.7254 (tpt) REVERT: A 1129 ASP cc_start: 0.7980 (t70) cc_final: 0.7692 (t0) REVERT: A 1141 GLU cc_start: 0.7710 (tp30) cc_final: 0.7316 (tp30) REVERT: A 1232 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: A 1251 GLU cc_start: 0.7838 (tp30) cc_final: 0.7488 (tp30) REVERT: B 69 ASP cc_start: 0.8877 (t70) cc_final: 0.8522 (t0) REVERT: B 100 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8363 (ptp) REVERT: B 133 CYS cc_start: 0.7264 (m) cc_final: 0.6877 (t) REVERT: B 1107 MET cc_start: 0.7393 (ttm) cc_final: 0.7109 (ttm) REVERT: B 1141 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7659 (pt0) REVERT: B 1181 ASN cc_start: 0.8019 (m-40) cc_final: 0.7186 (OUTLIER) REVERT: B 1239 ARG cc_start: 0.6639 (mpt-90) cc_final: 0.6099 (mmm-85) REVERT: B 1294 ASP cc_start: 0.8541 (m-30) cc_final: 0.8291 (m-30) REVERT: D 64 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7713 (mt-10) REVERT: D 66 LYS cc_start: 0.8711 (mtmm) cc_final: 0.8280 (mmtt) REVERT: D 105 LYS cc_start: 0.8186 (mtmt) cc_final: 0.7949 (ttmt) REVERT: D 160 GLU cc_start: 0.8116 (pm20) cc_final: 0.7810 (pm20) REVERT: D 187 GLU cc_start: 0.6264 (pm20) cc_final: 0.5913 (pm20) REVERT: D 204 LYS cc_start: 0.7716 (tttt) cc_final: 0.7417 (ttpt) REVERT: D 231 GLU cc_start: 0.7875 (pm20) cc_final: 0.7665 (mt-10) REVERT: D 232 GLN cc_start: 0.7913 (mt0) cc_final: 0.7478 (pt0) REVERT: D 236 ASP cc_start: 0.7632 (p0) cc_final: 0.7374 (m-30) REVERT: D 340 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7620 (mp) REVERT: D 467 LYS cc_start: 0.7553 (tppt) cc_final: 0.6529 (tptp) REVERT: E 28 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7198 (mmtm) REVERT: E 294 MET cc_start: 0.8447 (tmm) cc_final: 0.8182 (tmm) REVERT: E 309 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6693 (ttm) REVERT: E 345 GLU cc_start: 0.7136 (tt0) cc_final: 0.6683 (tm-30) REVERT: E 349 ARG cc_start: 0.7234 (mtm110) cc_final: 0.6858 (mtm-85) REVERT: E 380 ARG cc_start: 0.6857 (ptp90) cc_final: 0.6442 (mtt180) REVERT: E 428 ARG cc_start: 0.7238 (mmm-85) cc_final: 0.6974 (mtp85) REVERT: E 452 ARG cc_start: 0.8014 (mtt90) cc_final: 0.6956 (mmt-90) REVERT: E 467 LYS cc_start: 0.7610 (mttt) cc_final: 0.7199 (mtpm) REVERT: E 472 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7297 (tm-30) REVERT: E 487 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7239 (mm-30) REVERT: E 500 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7666 (mp0) outliers start: 32 outliers final: 18 residues processed: 256 average time/residue: 0.6309 time to fit residues: 180.7416 Evaluate side-chains 220 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 711 HIS Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 1232 GLU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1143 ILE Chi-restraints excluded: chain B residue 1283 VAL Chi-restraints excluded: chain B residue 1293 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 28 LYS Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 312 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0970 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1258 GLN D 245 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 ASN D 383 GLN E 100 ASN E 245 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.158357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.117856 restraints weight = 32978.985| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.97 r_work: 0.3372 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17522 Z= 0.140 Angle : 0.599 10.375 23804 Z= 0.315 Chirality : 0.044 0.228 2635 Planarity : 0.004 0.049 2881 Dihedral : 17.424 169.243 2827 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.72 % Allowed : 26.70 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 1935 helix: 1.79 (0.18), residues: 807 sheet: -0.41 (0.26), residues: 393 loop : -1.07 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 452 TYR 0.020 0.001 TYR A 212 PHE 0.034 0.001 PHE D 103 TRP 0.009 0.001 TRP E 243 HIS 0.004 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (17522) covalent geometry : angle 0.59937 / 0.32 (23804) hydrogen bonds : bond 0.04476 / 4.68 ( 801) hydrogen bonds : angle 5.04458 / 5.72 ( 2297) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 218 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 46 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7758 (mp) REVERT: A 62 LYS cc_start: 0.6639 (mmtt) cc_final: 0.5771 (mttp) REVERT: A 75 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7317 (mm-30) REVERT: A 92 GLU cc_start: 0.6787 (mp0) cc_final: 0.6294 (mp0) REVERT: A 133 CYS cc_start: 0.8187 (m) cc_final: 0.7670 (t) REVERT: A 202 LYS cc_start: 0.7661 (mttt) cc_final: 0.7370 (mtmt) REVERT: A 208 MET cc_start: 0.8427 (tpp) cc_final: 0.7607 (tmt) REVERT: A 1107 MET cc_start: 0.6964 (mmm) cc_final: 0.6475 (tpp) REVERT: A 1108 MET cc_start: 0.7484 (tpp) cc_final: 0.7148 (tpt) REVERT: A 1129 ASP cc_start: 0.7818 (t70) cc_final: 0.7492 (t0) REVERT: A 1141 GLU cc_start: 0.7494 (tp30) cc_final: 0.7163 (tp30) REVERT: A 1270 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7321 (t70) REVERT: B 7 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.7917 (ttm) REVERT: B 69 ASP cc_start: 0.8772 (t70) cc_final: 0.8312 (t0) REVERT: B 127 VAL cc_start: 0.6646 (t) cc_final: 0.6283 (m) REVERT: B 133 CYS cc_start: 0.7088 (m) cc_final: 0.6670 (t) REVERT: B 173 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7242 (tttp) REVERT: B 177 ASP cc_start: 0.8044 (p0) cc_final: 0.7802 (p0) REVERT: B 1107 MET cc_start: 0.7288 (ttm) cc_final: 0.7000 (tpp) REVERT: B 1141 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7524 (pt0) REVERT: B 1239 ARG cc_start: 0.6567 (mpt-90) cc_final: 0.5986 (mmm-85) REVERT: B 1264 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7750 (tt) REVERT: D 64 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7652 (mt-10) REVERT: D 66 LYS cc_start: 0.8607 (mtmm) cc_final: 0.8123 (mttt) REVERT: D 160 GLU cc_start: 0.8098 (pm20) cc_final: 0.7759 (pm20) REVERT: D 187 GLU cc_start: 0.6136 (pm20) cc_final: 0.5665 (pm20) REVERT: D 204 LYS cc_start: 0.7728 (tttt) cc_final: 0.7300 (ttpt) REVERT: D 218 GLN cc_start: 0.6678 (mm-40) cc_final: 0.6463 (mp10) REVERT: D 231 GLU cc_start: 0.7759 (pm20) cc_final: 0.7321 (mt-10) REVERT: D 232 GLN cc_start: 0.7856 (mt0) cc_final: 0.7445 (pt0) REVERT: D 236 ASP cc_start: 0.7550 (p0) cc_final: 0.7213 (m-30) REVERT: D 349 ARG cc_start: 0.7230 (ttp80) cc_final: 0.6910 (ttp80) REVERT: D 467 LYS cc_start: 0.7792 (tppt) cc_final: 0.6578 (tptp) REVERT: E 294 MET cc_start: 0.8439 (tmm) cc_final: 0.8087 (tmm) REVERT: E 342 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6384 (tp30) REVERT: E 345 GLU cc_start: 0.7153 (tt0) cc_final: 0.6722 (tm-30) REVERT: E 349 ARG cc_start: 0.7240 (mtm110) cc_final: 0.6960 (ttp-170) REVERT: E 380 ARG cc_start: 0.6915 (ptp90) cc_final: 0.6500 (mtt180) REVERT: E 428 ARG cc_start: 0.7551 (mmm-85) cc_final: 0.7101 (mtp85) REVERT: E 451 GLU cc_start: 0.6511 (tp30) cc_final: 0.6200 (tp30) REVERT: E 452 ARG cc_start: 0.7966 (mtt90) cc_final: 0.7744 (mtt-85) REVERT: E 467 LYS cc_start: 0.7866 (mttt) cc_final: 0.7248 (mtpm) REVERT: E 487 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7289 (mm-30) outliers start: 84 outliers final: 31 residues processed: 273 average time/residue: 0.6050 time to fit residues: 185.5510 Evaluate side-chains 235 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1270 ASP Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1143 ILE Chi-restraints excluded: chain B residue 1264 LEU Chi-restraints excluded: chain B residue 1283 VAL Chi-restraints excluded: chain B residue 1293 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 448 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 153 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 180 optimal weight: 0.0370 chunk 138 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 684 ASN ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1258 GLN ** D 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 HIS E 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.157709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.117734 restraints weight = 25790.100| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.63 r_work: 0.3413 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17522 Z= 0.143 Angle : 0.571 9.464 23804 Z= 0.299 Chirality : 0.043 0.268 2635 Planarity : 0.003 0.043 2881 Dihedral : 17.306 169.105 2800 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.38 % Allowed : 26.64 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.19), residues: 1935 helix: 2.01 (0.18), residues: 805 sheet: -0.23 (0.26), residues: 385 loop : -1.04 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1105 TYR 0.015 0.001 TYR A 212 PHE 0.015 0.001 PHE E 54 TRP 0.007 0.001 TRP A 164 HIS 0.003 0.001 HIS B1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (17522) covalent geometry : angle 0.57133 / 0.30 (23804) hydrogen bonds : bond 0.04057 / 4.25 ( 801) hydrogen bonds : angle 4.72167 / 5.38 ( 2297) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 205 time to evaluate : 0.654 Fit side-chains REVERT: A 62 LYS cc_start: 0.6527 (mmtt) cc_final: 0.5627 (mttp) REVERT: A 75 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7279 (mm-30) REVERT: A 92 GLU cc_start: 0.6539 (mp0) cc_final: 0.6193 (mp0) REVERT: A 132 LYS cc_start: 0.8034 (mtpt) cc_final: 0.7667 (ttmm) REVERT: A 133 CYS cc_start: 0.8113 (m) cc_final: 0.7699 (t) REVERT: A 140 MET cc_start: 0.7938 (ttm) cc_final: 0.7696 (ttt) REVERT: A 202 LYS cc_start: 0.7614 (mttt) cc_final: 0.7322 (mtmt) REVERT: A 208 MET cc_start: 0.8411 (tpp) cc_final: 0.7683 (tmm) REVERT: A 1107 MET cc_start: 0.7021 (mmm) cc_final: 0.6628 (tpp) REVERT: A 1108 MET cc_start: 0.7444 (tpp) cc_final: 0.7156 (tpt) REVERT: A 1129 ASP cc_start: 0.7724 (t70) cc_final: 0.7397 (t0) REVERT: A 1270 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7180 (t70) REVERT: A 1303 SER cc_start: 0.7947 (OUTLIER) cc_final: 0.7517 (p) REVERT: B 7 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.7859 (ttm) REVERT: B 92 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6704 (mp0) REVERT: B 127 VAL cc_start: 0.6543 (t) cc_final: 0.6158 (m) REVERT: B 133 CYS cc_start: 0.6968 (m) cc_final: 0.6558 (t) REVERT: B 173 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7070 (tttp) REVERT: B 177 ASP cc_start: 0.7965 (p0) cc_final: 0.7696 (p0) REVERT: B 1107 MET cc_start: 0.7222 (ttm) cc_final: 0.6955 (tpp) REVERT: B 1141 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7465 (pt0) REVERT: B 1239 ARG cc_start: 0.6487 (mpt-90) cc_final: 0.5892 (mmm-85) REVERT: B 1264 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7634 (tt) REVERT: D 51 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6278 (mm-30) REVERT: D 64 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7587 (mt-10) REVERT: D 66 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8019 (mttt) REVERT: D 87 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.5702 (ttm170) REVERT: D 160 GLU cc_start: 0.8077 (pm20) cc_final: 0.7739 (pm20) REVERT: D 204 LYS cc_start: 0.7714 (tttt) cc_final: 0.7263 (ttpt) REVERT: D 218 GLN cc_start: 0.6630 (mm-40) cc_final: 0.6394 (mp10) REVERT: D 231 GLU cc_start: 0.7735 (pm20) cc_final: 0.7286 (mt-10) REVERT: D 232 GLN cc_start: 0.7900 (mt0) cc_final: 0.7513 (pt0) REVERT: D 236 ASP cc_start: 0.7522 (p0) cc_final: 0.7259 (m-30) REVERT: D 467 LYS cc_start: 0.7791 (tppt) cc_final: 0.6565 (tptp) REVERT: E 294 MET cc_start: 0.8392 (tmm) cc_final: 0.8013 (tmm) REVERT: E 342 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.6335 (tp30) REVERT: E 345 GLU cc_start: 0.7086 (tt0) cc_final: 0.6659 (tm-30) REVERT: E 349 ARG cc_start: 0.7217 (mtm110) cc_final: 0.6908 (ttp-170) REVERT: E 380 ARG cc_start: 0.6852 (ptp90) cc_final: 0.6428 (mtt90) REVERT: E 428 ARG cc_start: 0.7507 (mmm-85) cc_final: 0.7096 (mtp85) REVERT: E 451 GLU cc_start: 0.6663 (tp30) cc_final: 0.6361 (tp30) REVERT: E 452 ARG cc_start: 0.7974 (mtt90) cc_final: 0.7745 (mtt-85) REVERT: E 467 LYS cc_start: 0.7776 (mttt) cc_final: 0.7037 (mtpt) REVERT: E 471 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7118 (tp30) REVERT: E 487 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7273 (mm-30) REVERT: E 500 GLU cc_start: 0.8195 (tp30) cc_final: 0.7816 (mp0) outliers start: 78 outliers final: 40 residues processed: 261 average time/residue: 0.6084 time to fit residues: 177.5899 Evaluate side-chains 246 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1270 ASP Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1143 ILE Chi-restraints excluded: chain B residue 1167 SER Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1187 VAL Chi-restraints excluded: chain B residue 1193 THR Chi-restraints excluded: chain B residue 1264 LEU Chi-restraints excluded: chain B residue 1283 VAL Chi-restraints excluded: chain B residue 1293 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 448 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 33 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 8 optimal weight: 0.0770 chunk 69 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 chunk 53 optimal weight: 0.0040 chunk 125 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.5752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1258 GLN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.158488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119649 restraints weight = 25735.517| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.67 r_work: 0.3404 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 17522 Z= 0.116 Angle : 0.549 9.973 23804 Z= 0.288 Chirality : 0.042 0.203 2635 Planarity : 0.003 0.041 2881 Dihedral : 17.206 168.480 2798 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.67 % Allowed : 26.64 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 1935 helix: 2.09 (0.18), residues: 803 sheet: -0.04 (0.26), residues: 381 loop : -0.97 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1105 TYR 0.011 0.001 TYR A 212 PHE 0.020 0.001 PHE E 484 TRP 0.007 0.001 TRP A 164 HIS 0.003 0.001 HIS E 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (17522) covalent geometry : angle 0.54928 / 0.29 (23804) hydrogen bonds : bond 0.03740 / 3.90 ( 801) hydrogen bonds : angle 4.54054 / 5.20 ( 2297) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 207 time to evaluate : 0.615 Fit side-chains REVERT: A 62 LYS cc_start: 0.6334 (mmtt) cc_final: 0.5476 (mttp) REVERT: A 75 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7195 (mm-30) REVERT: A 92 GLU cc_start: 0.6366 (mp0) cc_final: 0.6023 (mp0) REVERT: A 132 LYS cc_start: 0.7896 (mtpt) cc_final: 0.7495 (ttmm) REVERT: A 133 CYS cc_start: 0.8062 (m) cc_final: 0.7689 (t) REVERT: A 140 MET cc_start: 0.7843 (ttm) cc_final: 0.7640 (ttt) REVERT: A 202 LYS cc_start: 0.7603 (mttt) cc_final: 0.7315 (mtmt) REVERT: A 208 MET cc_start: 0.8415 (tpp) cc_final: 0.7811 (tmm) REVERT: A 1107 MET cc_start: 0.6946 (mmm) cc_final: 0.6483 (tpp) REVERT: A 1108 MET cc_start: 0.7414 (tpp) cc_final: 0.7122 (tpt) REVERT: A 1129 ASP cc_start: 0.7559 (t70) cc_final: 0.7268 (t0) REVERT: A 1251 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7379 (tp30) REVERT: A 1270 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.6961 (t70) REVERT: A 1303 SER cc_start: 0.7751 (OUTLIER) cc_final: 0.7336 (p) REVERT: B 7 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.7710 (ttm) REVERT: B 92 GLU cc_start: 0.6800 (mm-30) cc_final: 0.6574 (mp0) REVERT: B 127 VAL cc_start: 0.6399 (t) cc_final: 0.6010 (m) REVERT: B 133 CYS cc_start: 0.6845 (m) cc_final: 0.6450 (t) REVERT: B 173 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.6901 (tttp) REVERT: B 177 ASP cc_start: 0.7802 (p0) cc_final: 0.7485 (p0) REVERT: B 1141 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7360 (pt0) REVERT: B 1239 ARG cc_start: 0.6321 (mpt-90) cc_final: 0.5742 (mmm-85) REVERT: D 49 GLU cc_start: 0.8113 (tt0) cc_final: 0.7704 (mt-10) REVERT: D 64 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7461 (mt-10) REVERT: D 66 LYS cc_start: 0.8430 (mtmm) cc_final: 0.7908 (mttt) REVERT: D 160 GLU cc_start: 0.8033 (pm20) cc_final: 0.7687 (pm20) REVERT: D 187 GLU cc_start: 0.6195 (pm20) cc_final: 0.5719 (pm20) REVERT: D 204 LYS cc_start: 0.7642 (tttt) cc_final: 0.7166 (ttpt) REVERT: D 218 GLN cc_start: 0.6458 (mm-40) cc_final: 0.6250 (mp10) REVERT: D 231 GLU cc_start: 0.7752 (pm20) cc_final: 0.7198 (mt-10) REVERT: D 232 GLN cc_start: 0.7787 (mt0) cc_final: 0.7375 (pt0) REVERT: D 236 ASP cc_start: 0.7358 (p0) cc_final: 0.7082 (m-30) REVERT: D 434 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7201 (mtpp) REVERT: D 467 LYS cc_start: 0.7700 (tppt) cc_final: 0.6466 (tptp) REVERT: E 294 MET cc_start: 0.8321 (tmm) cc_final: 0.7971 (tmm) REVERT: E 345 GLU cc_start: 0.6899 (tt0) cc_final: 0.6528 (tm-30) REVERT: E 349 ARG cc_start: 0.7127 (mtm110) cc_final: 0.6794 (ttp-170) REVERT: E 380 ARG cc_start: 0.6766 (ptp90) cc_final: 0.6354 (mtt180) REVERT: E 428 ARG cc_start: 0.7462 (mmm-85) cc_final: 0.6892 (mtp85) REVERT: E 431 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7296 (p0) REVERT: E 451 GLU cc_start: 0.6747 (tp30) cc_final: 0.6516 (tp30) REVERT: E 467 LYS cc_start: 0.7649 (mttt) cc_final: 0.7101 (mtpt) REVERT: E 471 GLU cc_start: 0.7636 (mm-30) cc_final: 0.6972 (tp30) REVERT: E 487 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7270 (mm-30) REVERT: E 500 GLU cc_start: 0.8224 (tp30) cc_final: 0.7819 (mp0) outliers start: 83 outliers final: 39 residues processed: 265 average time/residue: 0.6056 time to fit residues: 180.1113 Evaluate side-chains 242 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 689 LYS Chi-restraints excluded: chain F residue 711 HIS Chi-restraints excluded: chain F residue 750 LEU Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1270 ASP Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1167 SER Chi-restraints excluded: chain B residue 1187 VAL Chi-restraints excluded: chain B residue 1193 THR Chi-restraints excluded: chain B residue 1200 ARG Chi-restraints excluded: chain B residue 1283 VAL Chi-restraints excluded: chain B residue 1293 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 448 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 6 optimal weight: 0.0870 chunk 162 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 7 optimal weight: 0.3980 chunk 186 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 701 HIS B1258 GLN D 247 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.158882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.120041 restraints weight = 25863.210| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.72 r_work: 0.3431 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17522 Z= 0.124 Angle : 0.551 10.499 23804 Z= 0.287 Chirality : 0.043 0.331 2635 Planarity : 0.003 0.042 2881 Dihedral : 17.191 168.468 2794 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.50 % Allowed : 26.98 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.19), residues: 1935 helix: 2.15 (0.18), residues: 804 sheet: 0.03 (0.26), residues: 381 loop : -0.97 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 452 TYR 0.011 0.001 TYR B1162 PHE 0.026 0.001 PHE A1088 TRP 0.006 0.001 TRP A 164 HIS 0.004 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (17522) covalent geometry : angle 0.55132 / 0.29 (23804) hydrogen bonds : bond 0.03663 / 3.81 ( 801) hydrogen bonds : angle 4.42638 / 5.08 ( 2297) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 200 time to evaluate : 0.703 Fit side-chains REVERT: A 75 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7185 (mm-30) REVERT: A 92 GLU cc_start: 0.6322 (mp0) cc_final: 0.5994 (mp0) REVERT: A 101 VAL cc_start: 0.8013 (OUTLIER) cc_final: 0.7703 (t) REVERT: A 132 LYS cc_start: 0.7931 (mtpt) cc_final: 0.7495 (ttmm) REVERT: A 133 CYS cc_start: 0.8047 (m) cc_final: 0.7713 (t) REVERT: A 202 LYS cc_start: 0.7578 (mttt) cc_final: 0.7289 (mtmt) REVERT: A 208 MET cc_start: 0.8419 (tpp) cc_final: 0.7718 (tmm) REVERT: A 1107 MET cc_start: 0.6948 (mmm) cc_final: 0.6433 (tpp) REVERT: A 1108 MET cc_start: 0.7379 (tpp) cc_final: 0.7109 (tpt) REVERT: A 1129 ASP cc_start: 0.7482 (t70) cc_final: 0.7202 (t0) REVERT: A 1303 SER cc_start: 0.7721 (OUTLIER) cc_final: 0.7267 (p) REVERT: B 7 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.7702 (ttm) REVERT: B 92 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6582 (mp0) REVERT: B 127 VAL cc_start: 0.6371 (t) cc_final: 0.5965 (m) REVERT: B 133 CYS cc_start: 0.6830 (m) cc_final: 0.6445 (t) REVERT: B 173 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.6841 (ttpp) REVERT: B 177 ASP cc_start: 0.7766 (p0) cc_final: 0.7473 (p0) REVERT: B 1141 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7359 (pt0) REVERT: B 1239 ARG cc_start: 0.6326 (mpt-90) cc_final: 0.5736 (mmm-85) REVERT: B 1264 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7608 (tt) REVERT: D 49 GLU cc_start: 0.8071 (tt0) cc_final: 0.7659 (mt-10) REVERT: D 64 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7438 (mt-10) REVERT: D 66 LYS cc_start: 0.8401 (mtmm) cc_final: 0.7859 (mttt) REVERT: D 87 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.5491 (ttm170) REVERT: D 160 GLU cc_start: 0.8044 (pm20) cc_final: 0.7703 (pm20) REVERT: D 183 SER cc_start: 0.8103 (t) cc_final: 0.7775 (p) REVERT: D 187 GLU cc_start: 0.6254 (pm20) cc_final: 0.5784 (pm20) REVERT: D 204 LYS cc_start: 0.7650 (tttt) cc_final: 0.7173 (ttmm) REVERT: D 218 GLN cc_start: 0.6469 (mm-40) cc_final: 0.6261 (mp10) REVERT: D 232 GLN cc_start: 0.7828 (mt0) cc_final: 0.7440 (pt0) REVERT: D 236 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.7098 (m-30) REVERT: D 467 LYS cc_start: 0.7647 (tppt) cc_final: 0.6417 (tptp) REVERT: E 345 GLU cc_start: 0.6880 (tt0) cc_final: 0.6486 (tm-30) REVERT: E 380 ARG cc_start: 0.6798 (ptp90) cc_final: 0.6386 (mtt180) REVERT: E 428 ARG cc_start: 0.7430 (mmm-85) cc_final: 0.6878 (mtp85) REVERT: E 431 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7291 (p0) REVERT: E 467 LYS cc_start: 0.7716 (mttt) cc_final: 0.6966 (mtpt) REVERT: E 471 GLU cc_start: 0.7645 (mm-30) cc_final: 0.6965 (tp30) REVERT: E 472 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7389 (tm-30) REVERT: E 487 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7244 (mm-30) REVERT: E 500 GLU cc_start: 0.8252 (tp30) cc_final: 0.7815 (mp0) outliers start: 80 outliers final: 41 residues processed: 261 average time/residue: 0.5872 time to fit residues: 172.2595 Evaluate side-chains 241 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 192 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 689 LYS Chi-restraints excluded: chain F residue 750 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1143 ILE Chi-restraints excluded: chain B residue 1167 SER Chi-restraints excluded: chain B residue 1184 TYR Chi-restraints excluded: chain B residue 1187 VAL Chi-restraints excluded: chain B residue 1193 THR Chi-restraints excluded: chain B residue 1200 ARG Chi-restraints excluded: chain B residue 1264 LEU Chi-restraints excluded: chain B residue 1283 VAL Chi-restraints excluded: chain B residue 1293 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 431 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 86 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 166 optimal weight: 0.6980 chunk 35 optimal weight: 0.0770 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1258 GLN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 GLN ** E 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.159459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.120483 restraints weight = 27784.610| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.83 r_work: 0.3430 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17522 Z= 0.115 Angle : 0.541 10.444 23804 Z= 0.282 Chirality : 0.042 0.201 2635 Planarity : 0.003 0.043 2881 Dihedral : 17.143 168.407 2794 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.72 % Allowed : 26.98 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.19), residues: 1935 helix: 2.25 (0.18), residues: 804 sheet: 0.15 (0.26), residues: 381 loop : -0.93 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1105 TYR 0.012 0.001 TYR B1162 PHE 0.024 0.001 PHE A1088 TRP 0.006 0.001 TRP A 164 HIS 0.003 0.001 HIS D 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (17522) covalent geometry : angle 0.54086 / 0.28 (23804) hydrogen bonds : bond 0.03541 / 3.68 ( 801) hydrogen bonds : angle 4.34050 / 5.01 ( 2297) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 202 time to evaluate : 0.663 Fit side-chains REVERT: A 75 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7197 (mm-30) REVERT: A 92 GLU cc_start: 0.6321 (mp0) cc_final: 0.5981 (mp0) REVERT: A 101 VAL cc_start: 0.8009 (OUTLIER) cc_final: 0.7700 (t) REVERT: A 132 LYS cc_start: 0.7926 (mtpt) cc_final: 0.7483 (ttmm) REVERT: A 133 CYS cc_start: 0.8079 (m) cc_final: 0.7775 (t) REVERT: A 147 SER cc_start: 0.7308 (p) cc_final: 0.7063 (p) REVERT: A 202 LYS cc_start: 0.7580 (mttt) cc_final: 0.7286 (mtmt) REVERT: A 208 MET cc_start: 0.8457 (tpp) cc_final: 0.7621 (tmm) REVERT: A 1107 MET cc_start: 0.6964 (mmm) cc_final: 0.6431 (tpp) REVERT: A 1108 MET cc_start: 0.7358 (tpp) cc_final: 0.7092 (tpt) REVERT: A 1129 ASP cc_start: 0.7482 (t70) cc_final: 0.7205 (t0) REVERT: A 1140 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7684 (tpt) REVERT: A 1251 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7374 (tp30) REVERT: A 1270 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.6927 (t70) REVERT: A 1303 SER cc_start: 0.7784 (OUTLIER) cc_final: 0.7317 (p) REVERT: B 7 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.7607 (ttm) REVERT: B 92 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6618 (mp0) REVERT: B 127 VAL cc_start: 0.6327 (t) cc_final: 0.5919 (m) REVERT: B 133 CYS cc_start: 0.6833 (m) cc_final: 0.6460 (t) REVERT: B 173 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6857 (ttpp) REVERT: B 177 ASP cc_start: 0.7757 (p0) cc_final: 0.7462 (p0) REVERT: B 1108 MET cc_start: 0.7245 (mmt) cc_final: 0.6876 (tpp) REVERT: B 1141 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7337 (pt0) REVERT: B 1239 ARG cc_start: 0.6281 (mpt-90) cc_final: 0.5683 (mmm-85) REVERT: B 1264 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7600 (tt) REVERT: D 49 GLU cc_start: 0.8087 (tt0) cc_final: 0.7701 (mt-10) REVERT: D 64 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7435 (mt-10) REVERT: D 66 LYS cc_start: 0.8400 (mtmm) cc_final: 0.7847 (mttt) REVERT: D 87 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.5492 (ttm170) REVERT: D 160 GLU cc_start: 0.8034 (pm20) cc_final: 0.7691 (pm20) REVERT: D 183 SER cc_start: 0.8070 (t) cc_final: 0.7757 (p) REVERT: D 187 GLU cc_start: 0.6251 (pm20) cc_final: 0.5783 (pm20) REVERT: D 204 LYS cc_start: 0.7655 (tttt) cc_final: 0.7149 (ttmm) REVERT: D 232 GLN cc_start: 0.7821 (mt0) cc_final: 0.7422 (pt0) REVERT: D 236 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7127 (m-30) REVERT: D 467 LYS cc_start: 0.7608 (tppt) cc_final: 0.6433 (tptp) REVERT: E 345 GLU cc_start: 0.6864 (tt0) cc_final: 0.6407 (tm-30) REVERT: E 380 ARG cc_start: 0.6783 (ptp90) cc_final: 0.6397 (mtt90) REVERT: E 428 ARG cc_start: 0.7400 (mmm-85) cc_final: 0.6919 (mtp85) REVERT: E 431 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7299 (p0) REVERT: E 467 LYS cc_start: 0.7534 (mttt) cc_final: 0.6808 (mtpt) REVERT: E 471 GLU cc_start: 0.7653 (mm-30) cc_final: 0.6977 (tp30) REVERT: E 472 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7369 (tm-30) REVERT: E 487 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7263 (mm-30) REVERT: E 500 GLU cc_start: 0.8272 (tp30) cc_final: 0.7823 (mp0) outliers start: 84 outliers final: 47 residues processed: 263 average time/residue: 0.6088 time to fit residues: 179.2958 Evaluate side-chains 251 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 194 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 689 LYS Chi-restraints excluded: chain F residue 711 HIS Chi-restraints excluded: chain F residue 750 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1270 ASP Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1143 ILE Chi-restraints excluded: chain B residue 1167 SER Chi-restraints excluded: chain B residue 1187 VAL Chi-restraints excluded: chain B residue 1193 THR Chi-restraints excluded: chain B residue 1200 ARG Chi-restraints excluded: chain B residue 1264 LEU Chi-restraints excluded: chain B residue 1283 VAL Chi-restraints excluded: chain B residue 1293 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 431 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 133 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN D 218 GLN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 GLN ** E 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.158174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.119814 restraints weight = 23468.890| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.54 r_work: 0.3407 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17522 Z= 0.122 Angle : 0.552 10.845 23804 Z= 0.286 Chirality : 0.043 0.351 2635 Planarity : 0.003 0.043 2881 Dihedral : 17.145 168.557 2794 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.61 % Allowed : 27.09 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.19), residues: 1935 helix: 2.26 (0.18), residues: 804 sheet: 0.17 (0.26), residues: 381 loop : -0.92 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 452 TYR 0.010 0.001 TYR B1162 PHE 0.025 0.001 PHE A1088 TRP 0.006 0.001 TRP A 164 HIS 0.003 0.001 HIS E 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (17522) covalent geometry : angle 0.55157 / 0.29 (23804) hydrogen bonds : bond 0.03515 / 3.65 ( 801) hydrogen bonds : angle 4.29739 / 4.96 ( 2297) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 200 time to evaluate : 0.626 Fit side-chains REVERT: A 7 MET cc_start: 0.8288 (ttm) cc_final: 0.7885 (ttp) REVERT: A 46 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7518 (pt) REVERT: A 75 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7207 (mm-30) REVERT: A 92 GLU cc_start: 0.6432 (mp0) cc_final: 0.6093 (mp0) REVERT: A 101 VAL cc_start: 0.8002 (OUTLIER) cc_final: 0.7699 (t) REVERT: A 132 LYS cc_start: 0.7936 (mtpt) cc_final: 0.7706 (mtpp) REVERT: A 133 CYS cc_start: 0.8018 (m) cc_final: 0.7753 (t) REVERT: A 147 SER cc_start: 0.7330 (p) cc_final: 0.7088 (p) REVERT: A 202 LYS cc_start: 0.7597 (mttt) cc_final: 0.7321 (mtpt) REVERT: A 208 MET cc_start: 0.8454 (tpp) cc_final: 0.7743 (tmm) REVERT: A 1107 MET cc_start: 0.7020 (mmm) cc_final: 0.6489 (tpp) REVERT: A 1108 MET cc_start: 0.7394 (tpp) cc_final: 0.7136 (tpt) REVERT: A 1129 ASP cc_start: 0.7539 (t70) cc_final: 0.7259 (t0) REVERT: A 1140 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7813 (tpt) REVERT: A 1251 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7253 (tp30) REVERT: A 1270 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7043 (t70) REVERT: A 1303 SER cc_start: 0.7870 (OUTLIER) cc_final: 0.7413 (p) REVERT: B 7 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.7587 (ttm) REVERT: B 133 CYS cc_start: 0.6695 (m) cc_final: 0.6334 (t) REVERT: B 173 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6945 (ttpp) REVERT: B 177 ASP cc_start: 0.7877 (p0) cc_final: 0.7584 (p0) REVERT: B 208 MET cc_start: 0.7777 (tpp) cc_final: 0.7339 (tpt) REVERT: B 211 LYS cc_start: 0.8240 (pttp) cc_final: 0.7865 (pmtt) REVERT: B 1141 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7370 (pt0) REVERT: B 1239 ARG cc_start: 0.6395 (mpt-90) cc_final: 0.5808 (mmm-85) REVERT: D 49 GLU cc_start: 0.8108 (tt0) cc_final: 0.7708 (mt-10) REVERT: D 64 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7475 (mt-10) REVERT: D 66 LYS cc_start: 0.8448 (mtmm) cc_final: 0.7893 (mttt) REVERT: D 87 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.5549 (ttm170) REVERT: D 160 GLU cc_start: 0.8061 (pm20) cc_final: 0.7720 (pm20) REVERT: D 183 SER cc_start: 0.8179 (t) cc_final: 0.7728 (p) REVERT: D 187 GLU cc_start: 0.6264 (pm20) cc_final: 0.5798 (pm20) REVERT: D 204 LYS cc_start: 0.7706 (tttt) cc_final: 0.7185 (ttmm) REVERT: D 232 GLN cc_start: 0.7869 (mt0) cc_final: 0.7420 (pt0) REVERT: D 236 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.7142 (m-30) REVERT: D 467 LYS cc_start: 0.7637 (tppt) cc_final: 0.6476 (tptp) REVERT: E 98 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8727 (t) REVERT: E 345 GLU cc_start: 0.6899 (tt0) cc_final: 0.6393 (tm-30) REVERT: E 380 ARG cc_start: 0.6819 (ptp90) cc_final: 0.6422 (mtt90) REVERT: E 431 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7310 (p0) REVERT: E 467 LYS cc_start: 0.7521 (mttt) cc_final: 0.6793 (mtpt) REVERT: E 471 GLU cc_start: 0.7655 (mm-30) cc_final: 0.6983 (tp30) REVERT: E 472 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7382 (tm-30) REVERT: E 487 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7302 (mm-30) REVERT: E 500 GLU cc_start: 0.8321 (tp30) cc_final: 0.7845 (mp0) outliers start: 82 outliers final: 47 residues processed: 259 average time/residue: 0.5875 time to fit residues: 170.7730 Evaluate side-chains 251 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 193 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 689 LYS Chi-restraints excluded: chain F residue 711 HIS Chi-restraints excluded: chain F residue 750 LEU Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1270 ASP Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1143 ILE Chi-restraints excluded: chain B residue 1167 SER Chi-restraints excluded: chain B residue 1187 VAL Chi-restraints excluded: chain B residue 1193 THR Chi-restraints excluded: chain B residue 1200 ARG Chi-restraints excluded: chain B residue 1228 ILE Chi-restraints excluded: chain B residue 1283 VAL Chi-restraints excluded: chain B residue 1293 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 431 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 30 optimal weight: 0.1980 chunk 46 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN ** B1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 GLN D 219 ASN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.158444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119595 restraints weight = 25636.982| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.67 r_work: 0.3404 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17522 Z= 0.116 Angle : 0.551 11.462 23804 Z= 0.285 Chirality : 0.043 0.341 2635 Planarity : 0.003 0.044 2881 Dihedral : 17.123 168.599 2794 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.27 % Allowed : 27.54 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 1935 helix: 2.31 (0.18), residues: 804 sheet: 0.22 (0.26), residues: 381 loop : -0.90 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 452 TYR 0.011 0.001 TYR B1162 PHE 0.025 0.001 PHE E 484 TRP 0.006 0.001 TRP A 164 HIS 0.003 0.000 HIS D 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (17522) covalent geometry : angle 0.55141 / 0.29 (23804) hydrogen bonds : bond 0.03478 / 3.63 ( 801) hydrogen bonds : angle 4.27392 / 4.94 ( 2297) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 196 time to evaluate : 0.682 Fit side-chains REVERT: A 7 MET cc_start: 0.8302 (ttm) cc_final: 0.7952 (ttp) REVERT: A 56 ASP cc_start: 0.7912 (m-30) cc_final: 0.7585 (m-30) REVERT: A 75 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7201 (mm-30) REVERT: A 92 GLU cc_start: 0.6430 (mp0) cc_final: 0.6083 (mp0) REVERT: A 132 LYS cc_start: 0.7922 (mtpt) cc_final: 0.7714 (mtpp) REVERT: A 133 CYS cc_start: 0.8005 (m) cc_final: 0.7787 (t) REVERT: A 147 SER cc_start: 0.7357 (p) cc_final: 0.7101 (p) REVERT: A 202 LYS cc_start: 0.7613 (mttt) cc_final: 0.7334 (mtpt) REVERT: A 208 MET cc_start: 0.8464 (tpp) cc_final: 0.7757 (tmm) REVERT: A 1107 MET cc_start: 0.7004 (mmm) cc_final: 0.6782 (mmm) REVERT: A 1108 MET cc_start: 0.7370 (tpp) cc_final: 0.7117 (tpt) REVERT: A 1129 ASP cc_start: 0.7544 (t70) cc_final: 0.7264 (t0) REVERT: A 1251 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7249 (tp30) REVERT: A 1303 SER cc_start: 0.7855 (OUTLIER) cc_final: 0.7393 (p) REVERT: B 7 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.7543 (ttm) REVERT: B 127 VAL cc_start: 0.6506 (t) cc_final: 0.6028 (m) REVERT: B 133 CYS cc_start: 0.6678 (m) cc_final: 0.6334 (t) REVERT: B 173 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.6890 (ttpp) REVERT: B 177 ASP cc_start: 0.7881 (p0) cc_final: 0.7588 (p0) REVERT: B 208 MET cc_start: 0.7749 (tpp) cc_final: 0.7219 (tpt) REVERT: B 211 LYS cc_start: 0.8295 (pttp) cc_final: 0.7877 (pmtt) REVERT: B 1108 MET cc_start: 0.7284 (mmt) cc_final: 0.6826 (tpp) REVERT: B 1141 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7388 (pt0) REVERT: B 1239 ARG cc_start: 0.6408 (mpt-90) cc_final: 0.5813 (mmm-85) REVERT: D 49 GLU cc_start: 0.8112 (tt0) cc_final: 0.7700 (mt-10) REVERT: D 64 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7480 (mt-10) REVERT: D 66 LYS cc_start: 0.8453 (mtmm) cc_final: 0.7899 (mttt) REVERT: D 87 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.5558 (ttm170) REVERT: D 160 GLU cc_start: 0.8071 (pm20) cc_final: 0.7729 (pm20) REVERT: D 183 SER cc_start: 0.8155 (t) cc_final: 0.7585 (p) REVERT: D 187 GLU cc_start: 0.6238 (pm20) cc_final: 0.5786 (pm20) REVERT: D 204 LYS cc_start: 0.7713 (tttt) cc_final: 0.7185 (ttmm) REVERT: D 232 GLN cc_start: 0.7878 (mt0) cc_final: 0.7476 (pt0) REVERT: D 236 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7143 (m-30) REVERT: D 467 LYS cc_start: 0.7635 (tppt) cc_final: 0.6470 (tptp) REVERT: D 502 ARG cc_start: 0.7224 (mmp-170) cc_final: 0.6491 (ttm110) REVERT: E 98 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8750 (t) REVERT: E 345 GLU cc_start: 0.6950 (tt0) cc_final: 0.6488 (tm-30) REVERT: E 380 ARG cc_start: 0.6800 (ptp90) cc_final: 0.6413 (mtt90) REVERT: E 428 ARG cc_start: 0.7418 (mmm-85) cc_final: 0.6543 (mtp85) REVERT: E 467 LYS cc_start: 0.7506 (mttt) cc_final: 0.6777 (mtpt) REVERT: E 471 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7194 (tp30) REVERT: E 472 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7372 (tm-30) REVERT: E 487 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7312 (mm-30) REVERT: E 500 GLU cc_start: 0.8331 (tp30) cc_final: 0.7859 (mp0) outliers start: 76 outliers final: 47 residues processed: 254 average time/residue: 0.5966 time to fit residues: 170.0293 Evaluate side-chains 241 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 689 LYS Chi-restraints excluded: chain F residue 750 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 1096 GLN Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1143 ILE Chi-restraints excluded: chain B residue 1167 SER Chi-restraints excluded: chain B residue 1187 VAL Chi-restraints excluded: chain B residue 1193 THR Chi-restraints excluded: chain B residue 1200 ARG Chi-restraints excluded: chain B residue 1228 ILE Chi-restraints excluded: chain B residue 1283 VAL Chi-restraints excluded: chain B residue 1293 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 379 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 105 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.0060 chunk 38 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 184 optimal weight: 0.2980 chunk 76 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN ** B1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS ** E 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.158834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.119057 restraints weight = 31822.347| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.03 r_work: 0.3371 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17522 Z= 0.129 Angle : 0.571 12.186 23804 Z= 0.292 Chirality : 0.043 0.283 2635 Planarity : 0.003 0.043 2881 Dihedral : 17.143 168.897 2794 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.99 % Allowed : 27.77 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.19), residues: 1935 helix: 2.24 (0.18), residues: 804 sheet: 0.22 (0.26), residues: 381 loop : -0.90 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 452 TYR 0.010 0.001 TYR B1162 PHE 0.020 0.001 PHE D 237 TRP 0.006 0.001 TRP A 164 HIS 0.003 0.001 HIS D 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (17522) covalent geometry : angle 0.57122 / 0.29 (23804) hydrogen bonds : bond 0.03519 / 3.68 ( 801) hydrogen bonds : angle 4.26669 / 4.95 ( 2297) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 190 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 7 MET cc_start: 0.8337 (ttm) cc_final: 0.7996 (ttp) REVERT: A 56 ASP cc_start: 0.7955 (m-30) cc_final: 0.7629 (m-30) REVERT: A 75 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7216 (mm-30) REVERT: A 92 GLU cc_start: 0.6467 (mp0) cc_final: 0.5980 (mp0) REVERT: A 132 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7684 (mtpp) REVERT: A 147 SER cc_start: 0.7340 (p) cc_final: 0.7081 (p) REVERT: A 178 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7209 (pt0) REVERT: A 202 LYS cc_start: 0.7619 (mttt) cc_final: 0.7338 (mtpt) REVERT: A 208 MET cc_start: 0.8428 (tpp) cc_final: 0.7646 (tmm) REVERT: A 1129 ASP cc_start: 0.7525 (t70) cc_final: 0.7259 (t0) REVERT: A 1251 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7279 (tp30) REVERT: A 1270 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7110 (t70) REVERT: A 1303 SER cc_start: 0.7862 (OUTLIER) cc_final: 0.7389 (p) REVERT: B 7 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.7556 (ttm) REVERT: B 127 VAL cc_start: 0.6528 (t) cc_final: 0.6064 (m) REVERT: B 133 CYS cc_start: 0.6698 (m) cc_final: 0.6323 (t) REVERT: B 173 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6984 (ttpp) REVERT: B 177 ASP cc_start: 0.7908 (p0) cc_final: 0.7562 (p0) REVERT: B 208 MET cc_start: 0.7763 (tpp) cc_final: 0.7282 (tpt) REVERT: B 211 LYS cc_start: 0.8287 (pttp) cc_final: 0.7888 (pmtt) REVERT: B 1102 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7161 (pt0) REVERT: B 1108 MET cc_start: 0.7228 (mmt) cc_final: 0.6774 (tpp) REVERT: B 1141 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7405 (pt0) REVERT: B 1239 ARG cc_start: 0.6436 (mpt-90) cc_final: 0.5838 (mmm-85) REVERT: D 49 GLU cc_start: 0.8138 (tt0) cc_final: 0.7722 (mt-10) REVERT: D 64 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7511 (mt-10) REVERT: D 66 LYS cc_start: 0.8464 (mtmm) cc_final: 0.7923 (mttt) REVERT: D 87 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.5576 (ttm170) REVERT: D 160 GLU cc_start: 0.8096 (pm20) cc_final: 0.7745 (pm20) REVERT: D 183 SER cc_start: 0.8131 (t) cc_final: 0.7633 (p) REVERT: D 187 GLU cc_start: 0.6234 (pm20) cc_final: 0.5786 (pm20) REVERT: D 204 LYS cc_start: 0.7721 (tttt) cc_final: 0.7162 (ttpt) REVERT: D 232 GLN cc_start: 0.7879 (mt0) cc_final: 0.7476 (pt0) REVERT: D 236 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7185 (m-30) REVERT: D 338 GLU cc_start: 0.5657 (OUTLIER) cc_final: 0.5370 (mp0) REVERT: D 467 LYS cc_start: 0.7639 (tppt) cc_final: 0.6469 (tptp) REVERT: D 502 ARG cc_start: 0.7254 (mmp-170) cc_final: 0.6474 (ttm110) REVERT: E 345 GLU cc_start: 0.6850 (tt0) cc_final: 0.6386 (tm-30) REVERT: E 380 ARG cc_start: 0.6854 (ptp90) cc_final: 0.6471 (mtt90) REVERT: E 428 ARG cc_start: 0.6885 (mmm-85) cc_final: 0.6062 (mtp85) REVERT: E 467 LYS cc_start: 0.7505 (mttt) cc_final: 0.6776 (mtpt) REVERT: E 471 GLU cc_start: 0.7666 (mm-30) cc_final: 0.6996 (tp30) REVERT: E 472 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7387 (tm-30) REVERT: E 487 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7308 (mm-30) REVERT: E 500 GLU cc_start: 0.8334 (tp30) cc_final: 0.7614 (mp0) REVERT: E 503 ARG cc_start: 0.5574 (OUTLIER) cc_final: 0.5238 (mtm180) outliers start: 71 outliers final: 48 residues processed: 244 average time/residue: 0.6119 time to fit residues: 166.8920 Evaluate side-chains 244 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 187 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 689 LYS Chi-restraints excluded: chain F residue 711 HIS Chi-restraints excluded: chain F residue 750 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 1096 GLN Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1270 ASP Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 1102 GLU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1143 ILE Chi-restraints excluded: chain B residue 1167 SER Chi-restraints excluded: chain B residue 1187 VAL Chi-restraints excluded: chain B residue 1193 THR Chi-restraints excluded: chain B residue 1200 ARG Chi-restraints excluded: chain B residue 1228 ILE Chi-restraints excluded: chain B residue 1283 VAL Chi-restraints excluded: chain B residue 1293 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 503 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 150 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 HIS ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.155093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.117343 restraints weight = 25564.191| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.56 r_work: 0.3393 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17522 Z= 0.202 Angle : 0.626 12.042 23804 Z= 0.321 Chirality : 0.046 0.342 2635 Planarity : 0.004 0.041 2881 Dihedral : 17.313 170.483 2794 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.54 % Allowed : 28.44 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 1935 helix: 2.13 (0.18), residues: 799 sheet: -0.06 (0.26), residues: 383 loop : -0.95 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 483 TYR 0.012 0.001 TYR A 185 PHE 0.026 0.002 PHE E 484 TRP 0.007 0.001 TRP A1151 HIS 0.005 0.001 HIS B1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (17522) covalent geometry : angle 0.62573 / 0.32 (23804) hydrogen bonds : bond 0.03973 / 4.17 ( 801) hydrogen bonds : angle 4.39224 / 5.09 ( 2297) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 192 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 56 ASP cc_start: 0.8093 (m-30) cc_final: 0.7845 (m-30) REVERT: A 75 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7345 (mm-30) REVERT: A 92 GLU cc_start: 0.6679 (mp0) cc_final: 0.6183 (mp0) REVERT: A 132 LYS cc_start: 0.7976 (mtpt) cc_final: 0.7609 (ttmm) REVERT: A 147 SER cc_start: 0.7699 (p) cc_final: 0.7466 (p) REVERT: A 190 GLU cc_start: 0.7790 (tt0) cc_final: 0.7563 (tp30) REVERT: A 202 LYS cc_start: 0.7757 (mttt) cc_final: 0.7436 (mtpt) REVERT: A 208 MET cc_start: 0.8498 (tpp) cc_final: 0.7822 (tmm) REVERT: A 1129 ASP cc_start: 0.7738 (t70) cc_final: 0.7463 (t0) REVERT: A 1303 SER cc_start: 0.8012 (OUTLIER) cc_final: 0.7511 (p) REVERT: B 5 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: B 7 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.7849 (ttm) REVERT: B 133 CYS cc_start: 0.6870 (m) cc_final: 0.6485 (t) REVERT: B 173 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7245 (ttpp) REVERT: B 177 ASP cc_start: 0.8061 (p0) cc_final: 0.7775 (p0) REVERT: B 208 MET cc_start: 0.7847 (tpp) cc_final: 0.7638 (tpt) REVERT: B 1108 MET cc_start: 0.7367 (mmt) cc_final: 0.6895 (tpp) REVERT: B 1115 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7090 (mm-30) REVERT: B 1141 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7627 (pt0) REVERT: B 1239 ARG cc_start: 0.6701 (mpt-90) cc_final: 0.6079 (mmm-85) REVERT: D 26 MET cc_start: 0.8423 (mmt) cc_final: 0.8108 (tpp) REVERT: D 49 GLU cc_start: 0.8125 (tt0) cc_final: 0.7748 (mt-10) REVERT: D 64 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7629 (mt-10) REVERT: D 66 LYS cc_start: 0.8619 (mtmm) cc_final: 0.8126 (mttt) REVERT: D 87 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.5811 (ttm170) REVERT: D 160 GLU cc_start: 0.8131 (pm20) cc_final: 0.7796 (pm20) REVERT: D 183 SER cc_start: 0.8215 (t) cc_final: 0.7800 (p) REVERT: D 187 GLU cc_start: 0.6422 (pm20) cc_final: 0.5930 (pm20) REVERT: D 204 LYS cc_start: 0.7888 (tttt) cc_final: 0.7361 (ttpt) REVERT: D 232 GLN cc_start: 0.7984 (mt0) cc_final: 0.7578 (pt0) REVERT: D 338 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.5508 (mp0) REVERT: D 467 LYS cc_start: 0.7770 (tppt) cc_final: 0.6619 (tptp) REVERT: D 502 ARG cc_start: 0.7244 (mmp-170) cc_final: 0.6483 (ttm110) REVERT: E 345 GLU cc_start: 0.7062 (tt0) cc_final: 0.6604 (tm-30) REVERT: E 380 ARG cc_start: 0.6993 (ptp90) cc_final: 0.6649 (mtt90) REVERT: E 428 ARG cc_start: 0.7084 (mmm-85) cc_final: 0.6279 (mtp85) REVERT: E 467 LYS cc_start: 0.7624 (mttt) cc_final: 0.6867 (mtpt) REVERT: E 471 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7306 (tp30) REVERT: E 472 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7472 (tm-30) REVERT: E 487 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7388 (mm-30) REVERT: E 500 GLU cc_start: 0.8388 (tp30) cc_final: 0.7615 (mp0) REVERT: E 503 ARG cc_start: 0.5652 (OUTLIER) cc_final: 0.5306 (mtm180) outliers start: 63 outliers final: 45 residues processed: 240 average time/residue: 0.6270 time to fit residues: 167.6475 Evaluate side-chains 239 residues out of total 1777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 711 HIS Chi-restraints excluded: chain F residue 750 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 1096 GLN Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1303 SER Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1137 SER Chi-restraints excluded: chain B residue 1143 ILE Chi-restraints excluded: chain B residue 1167 SER Chi-restraints excluded: chain B residue 1187 VAL Chi-restraints excluded: chain B residue 1193 THR Chi-restraints excluded: chain B residue 1200 ARG Chi-restraints excluded: chain B residue 1283 VAL Chi-restraints excluded: chain B residue 1293 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 294 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 503 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 90 optimal weight: 5.9990 chunk 166 optimal weight: 0.6980 chunk 182 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN ** B1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS E 245 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.157648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.119827 restraints weight = 26046.757| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.60 r_work: 0.3434 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17522 Z= 0.122 Angle : 0.572 12.226 23804 Z= 0.294 Chirality : 0.042 0.190 2635 Planarity : 0.003 0.043 2881 Dihedral : 17.178 169.308 2794 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.92 % Allowed : 29.17 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.19), residues: 1935 helix: 2.12 (0.18), residues: 811 sheet: -0.02 (0.26), residues: 382 loop : -0.92 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 483 TYR 0.010 0.001 TYR B1162 PHE 0.015 0.001 PHE D 237 TRP 0.007 0.001 TRP A 164 HIS 0.002 0.001 HIS D 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (17522) covalent geometry : angle 0.57163 / 0.29 (23804) hydrogen bonds : bond 0.03593 / 3.76 ( 801) hydrogen bonds : angle 4.32123 / 5.01 ( 2297) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6846.65 seconds wall clock time: 117 minutes 35.37 seconds (7055.37 seconds total)