Starting phenix.real_space_refine on Sat Jul 4 16:08:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oye_71016/07_2026/9oye_71016.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oye_71016/07_2026/9oye_71016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oye_71016/07_2026/9oye_71016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oye_71016/07_2026/9oye_71016.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oye_71016/07_2026/9oye_71016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oye_71016/07_2026/9oye_71016.map" } resolution = 2.72 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= 0.018 sd= 0.735 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 90 5.49 5 Mg 3 5.21 5 S 112 5.16 5 C 13266 2.51 5 N 3859 2.21 5 O 4183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 21517 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2726 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "B" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2840 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 16, 'TRANS': 348} Chain: "C" Number of atoms: 2873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2873 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 17, 'TRANS': 351} Chain: "D" Number of atoms: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2799 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "E" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2602 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "F" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2835 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 20, 'TRANS': 344} Chain: "G" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2844 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 345} Chain: "H" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 843 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "I" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 238 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "M" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3209 SG CYS B 64 29.308 83.145 37.408 1.00 44.70 S ATOM 3269 SG CYS B 73 25.529 82.950 37.758 1.00 49.18 S ATOM 3286 SG CYS B 76 27.105 80.339 36.186 1.00 69.39 S ATOM 3308 SG CYS B 79 27.903 80.815 40.075 1.00 50.40 S ATOM 6057 SG CYS C 64 9.167 57.743 70.697 1.00 43.40 S ATOM 6117 SG CYS C 73 7.425 55.435 73.239 1.00 45.42 S ATOM 6134 SG CYS C 76 8.592 53.979 70.321 1.00 69.79 S ATOM 6156 SG CYS C 79 11.334 55.424 72.739 1.00 49.94 S ATOM 8922 SG CYS D 64 34.388 32.422 101.044 1.00 39.75 S ATOM 8982 SG CYS D 73 36.423 30.036 103.022 1.00 49.67 S ATOM 8999 SG CYS D 76 37.277 30.327 99.361 1.00 42.61 S ATOM 9021 SG CYS D 79 38.086 33.225 101.461 1.00 47.06 S ATOM 11645 SG CYS E 50 80.884 35.452 101.970 1.00 44.94 S ATOM 11714 SG CYS E 59 84.268 34.118 101.016 1.00 44.75 S ATOM 11734 SG CYS E 62 81.569 34.054 98.410 1.00 44.81 S ATOM 11755 SG CYS E 65 82.805 37.378 99.363 1.00 46.30 S Time building chain proxies: 4.79, per 1000 atoms: 0.22 Number of scatterers: 21517 At special positions: 0 Unit cell: (121.716, 121.716, 150.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 112 16.00 P 90 15.00 Mg 3 11.99 O 4183 8.00 N 3859 7.00 C 13266 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 861.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 76 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 64 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 79 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 76 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 73 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 64 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 79 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 76 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 73 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 79 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 64 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 62 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 65 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 59 " Number of angles added : 24 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 15 sheets defined 56.3% alpha, 15.0% beta 40 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 5 through 7 No H-bonds generated for 'chain 'A' and resid 5 through 7' Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 27 through 45 Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.562A pdb=" N ILE A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 104 removed outlier: 3.716A pdb=" N GLU A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 124 through 131 removed outlier: 3.622A pdb=" N ALA A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.518A pdb=" N GLN A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 225 through 240 Processing helix chain 'A' and resid 242 through 264 removed outlier: 3.603A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 279 through 293 removed outlier: 4.339A pdb=" N GLY A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N MET A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 315 Processing helix chain 'A' and resid 320 through 332 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.570A pdb=" N VAL B 18 " --> pdb=" O PHE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 50 through 64 Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 100 through 110 removed outlier: 3.583A pdb=" N ASN B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 128 through 131 Processing helix chain 'B' and resid 132 through 145 removed outlier: 4.484A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 163 through 169 removed outlier: 3.889A pdb=" N LEU B 167 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG B 169 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.862A pdb=" N GLU B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 247 through 258 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 277 through 298 Processing helix chain 'B' and resid 299 through 302 Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.932A pdb=" N ALA B 307 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 321 through 339 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 344 through 358 Processing helix chain 'C' and resid 5 through 10 Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.523A pdb=" N VAL C 18 " --> pdb=" O PHE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 35 Processing helix chain 'C' and resid 50 through 64 Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 100 through 110 removed outlier: 4.320A pdb=" N ASN C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 131 Processing helix chain 'C' and resid 132 through 145 removed outlier: 4.456A pdb=" N LYS C 141 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N THR C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 163 through 170 removed outlier: 3.549A pdb=" N ARG C 169 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS C 170 " --> pdb=" O ILE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 195 Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.990A pdb=" N GLU C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.625A pdb=" N ALA C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 277 through 298 Processing helix chain 'C' and resid 299 through 302 removed outlier: 3.957A pdb=" N LEU C 302 " --> pdb=" O PRO C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 299 through 302' Processing helix chain 'C' and resid 303 through 307 removed outlier: 3.565A pdb=" N ALA C 307 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 321 through 339 Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 344 through 359 Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 14 through 18 Processing helix chain 'D' and resid 21 through 35 Processing helix chain 'D' and resid 50 through 64 Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 128 through 131 Processing helix chain 'D' and resid 132 through 145 removed outlier: 4.763A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 163 through 170 Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 199 through 211 removed outlier: 3.819A pdb=" N GLU D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 228 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.527A pdb=" N ALA D 249 " --> pdb=" O ASP D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 274 Processing helix chain 'D' and resid 277 through 298 Processing helix chain 'D' and resid 299 through 302 removed outlier: 3.921A pdb=" N LEU D 302 " --> pdb=" O PRO D 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 299 through 302' Processing helix chain 'D' and resid 303 through 307 removed outlier: 3.820A pdb=" N ALA D 307 " --> pdb=" O ASN D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 321 through 339 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 344 through 358 removed outlier: 3.734A pdb=" N ALA D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 20 removed outlier: 4.646A pdb=" N ASP E 10 " --> pdb=" O TRP E 6 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER E 17 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 50 Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 89 through 101 removed outlier: 3.585A pdb=" N VAL E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 121 through 134 removed outlier: 4.710A pdb=" N LYS E 130 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N THR E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 152 through 158 Processing helix chain 'E' and resid 168 through 180 removed outlier: 3.676A pdb=" N ARG E 178 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU E 179 " --> pdb=" O TRP E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 197 through 206 removed outlier: 3.610A pdb=" N PHE E 205 " --> pdb=" O ALA E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 227 Proline residue: E 225 - end of helix Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 240 through 261 Processing helix chain 'E' and resid 270 through 281 Processing helix chain 'E' and resid 282 through 303 Processing helix chain 'E' and resid 307 through 323 Processing helix chain 'F' and resid 7 through 18 removed outlier: 4.428A pdb=" N LYS F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) Proline residue: F 13 - end of helix Processing helix chain 'F' and resid 27 through 30 Processing helix chain 'F' and resid 72 through 81 Processing helix chain 'F' and resid 112 through 116 Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.711A pdb=" N THR F 142 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N PHE F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 157 removed outlier: 3.666A pdb=" N GLY F 157 " --> pdb=" O TYR F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 207 Processing helix chain 'F' and resid 259 through 274 Processing helix chain 'F' and resid 321 through 332 Processing helix chain 'G' and resid 7 through 18 removed outlier: 4.676A pdb=" N LYS G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) Proline residue: G 13 - end of helix Processing helix chain 'G' and resid 27 through 30 Processing helix chain 'G' and resid 72 through 82 removed outlier: 3.582A pdb=" N LEU G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 143 removed outlier: 3.591A pdb=" N THR G 142 " --> pdb=" O LEU G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 146 No H-bonds generated for 'chain 'G' and resid 144 through 146' Processing helix chain 'G' and resid 152 through 155 Processing helix chain 'G' and resid 197 through 207 Processing helix chain 'G' and resid 243 through 248 Processing helix chain 'G' and resid 260 through 271 Processing helix chain 'G' and resid 321 through 332 removed outlier: 3.588A pdb=" N LYS G 332 " --> pdb=" O LEU G 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 13 Processing helix chain 'J' and resid 21 through 25 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 4.529A pdb=" N PHE A 47 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N THR A 79 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU A 49 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU A 81 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N HIS A 51 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU A 83 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N PHE A 53 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 162 removed outlier: 6.315A pdb=" N GLU A 161 " --> pdb=" O LEU A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.197A pdb=" N LYS B 121 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 153 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TYR B 123 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ALA B 155 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE B 125 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA B 40 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N PHE B 173 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 42 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 197 through 198 removed outlier: 6.732A pdb=" N ALA B 197 " --> pdb=" O VAL B 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 359 through 361 Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 94 removed outlier: 6.189A pdb=" N LYS C 121 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU C 153 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N TYR C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA C 155 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE C 125 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TYR C 41 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR C 156 " --> pdb=" O TYR C 41 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE C 43 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA C 40 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE C 173 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU C 42 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU C 175 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER C 44 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 90 through 94 removed outlier: 6.280A pdb=" N ILE D 91 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ASP D 126 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE D 93 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LYS D 121 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU D 153 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N TYR D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA D 155 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE D 125 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR D 41 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA D 40 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N PHE D 173 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU D 42 " --> pdb=" O PHE D 173 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 76 through 79 Processing sheet with id=AA9, first strand: chain 'F' and resid 2 through 6 removed outlier: 3.506A pdb=" N ARG F 96 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASN G 295 " --> pdb=" O GLY G 280 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLY G 280 " --> pdb=" O ASN G 295 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 3.724A pdb=" N GLY F 66 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN F 32 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N THR F 47 " --> pdb=" O ASN F 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 309 through 311 removed outlier: 3.718A pdb=" N SER F 311 " --> pdb=" O HIS F 255 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N HIS F 255 " --> pdb=" O SER F 311 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP F 351 " --> pdb=" O ALA F 357 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ALA F 357 " --> pdb=" O ASP F 351 " (cutoff:3.500A) removed outlier: 15.873A pdb=" N SER F 181 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 16.085A pdb=" N THR F 172 " --> pdb=" O SER F 181 " (cutoff:3.500A) removed outlier: 14.874A pdb=" N VAL F 170 " --> pdb=" O PRO F 183 " (cutoff:3.500A) removed outlier: 13.959A pdb=" N GLY F 185 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 13.468A pdb=" N ARG F 168 " --> pdb=" O GLY F 185 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N SER F 187 " --> pdb=" O GLU F 166 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N GLU F 166 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLY F 164 " --> pdb=" O PRO F 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 303 through 307 Processing sheet with id=AB4, first strand: chain 'G' and resid 2 through 6 Processing sheet with id=AB5, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.525A pdb=" N ASN G 32 " --> pdb=" O THR G 47 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N THR G 47 " --> pdb=" O ASN G 32 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 191 through 196 removed outlier: 5.908A pdb=" N GLY G 157 " --> pdb=" O THR G 172 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N THR G 172 " --> pdb=" O GLY G 157 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA G 357 " --> pdb=" O ASP G 351 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP G 351 " --> pdb=" O ALA G 357 " (cutoff:3.500A) 1131 hydrogen bonds defined for protein. 3225 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 206 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 4.23 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7288 1.36 - 1.51: 5898 1.51 - 1.66: 8699 1.66 - 1.80: 139 1.80 - 1.95: 47 Bond restraints: 22071 Sorted by residual: bond pdb=" O3B AGS B 702 " pdb=" PB AGS B 702 " ideal model delta sigma weight residual 1.673 1.590 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O3B AGS D 702 " pdb=" PB AGS D 702 " ideal model delta sigma weight residual 1.673 1.591 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" O3B AGS C 702 " pdb=" PB AGS C 702 " ideal model delta sigma weight residual 1.673 1.591 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" O3A AGS C 702 " pdb=" PA AGS C 702 " ideal model delta sigma weight residual 1.664 1.584 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" O3A AGS D 702 " pdb=" PA AGS D 702 " ideal model delta sigma weight residual 1.664 1.585 0.079 2.00e-02 2.50e+03 1.56e+01 ... (remaining 22066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 29739 2.02 - 4.04: 515 4.04 - 6.06: 33 6.06 - 8.08: 11 8.08 - 10.10: 8 Bond angle restraints: 30306 Sorted by residual: angle pdb=" N3 DT H 6 " pdb=" C4 DT H 6 " pdb=" O4 DT H 6 " ideal model delta sigma weight residual 119.90 122.69 -2.79 6.00e-01 2.78e+00 2.17e+01 angle pdb=" O4' DA M 17 " pdb=" C4' DA M 17 " pdb=" C3' DA M 17 " ideal model delta sigma weight residual 106.00 103.25 2.75 6.00e-01 2.78e+00 2.11e+01 angle pdb=" N3 DT M 14 " pdb=" C4 DT M 14 " pdb=" O4 DT M 14 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" O4 DT H 6 " pdb=" C4 DT H 6 " pdb=" C5 DT H 6 " ideal model delta sigma weight residual 124.90 121.95 2.95 7.00e-01 2.04e+00 1.78e+01 angle pdb=" N3 DT M 4 " pdb=" C4 DT M 4 " pdb=" O4 DT M 4 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 ... (remaining 30301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.40: 12624 32.40 - 64.81: 624 64.81 - 97.21: 43 97.21 - 129.62: 0 129.62 - 162.02: 4 Dihedral angle restraints: 13295 sinusoidal: 5963 harmonic: 7332 Sorted by residual: dihedral pdb=" CA LEU C 244 " pdb=" C LEU C 244 " pdb=" N ASP C 245 " pdb=" CA ASP C 245 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C4' DC H 20 " pdb=" C3' DC H 20 " pdb=" O3' DC H 20 " pdb=" P DT H 21 " ideal model delta sinusoidal sigma weight residual 220.00 57.98 162.02 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" C4' DG H 35 " pdb=" C3' DG H 35 " pdb=" O3' DG H 35 " pdb=" P DC H 36 " ideal model delta sinusoidal sigma weight residual 220.00 74.73 145.27 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 13292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3005 0.055 - 0.111: 442 0.111 - 0.166: 38 0.166 - 0.222: 1 0.222 - 0.277: 3 Chirality restraints: 3489 Sorted by residual: chirality pdb=" C3' AGS B 702 " pdb=" C2' AGS B 702 " pdb=" C4' AGS B 702 " pdb=" O3' AGS B 702 " both_signs ideal model delta sigma weight residual False -2.37 -2.65 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C3' AGS D 702 " pdb=" C2' AGS D 702 " pdb=" C4' AGS D 702 " pdb=" O3' AGS D 702 " both_signs ideal model delta sigma weight residual False -2.37 -2.65 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C3' AGS C 702 " pdb=" C2' AGS C 702 " pdb=" C4' AGS C 702 " pdb=" O3' AGS C 702 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 3486 not shown) Planarity restraints: 3649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET G 182 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO G 183 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO G 183 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 183 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 116 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO F 117 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO F 117 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 117 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 320 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO D 321 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 321 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 321 " 0.020 5.00e-02 4.00e+02 ... (remaining 3646 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 7 2.52 - 3.12: 15120 3.12 - 3.71: 34037 3.71 - 4.31: 47951 4.31 - 4.90: 80091 Nonbonded interactions: 177206 Sorted by model distance: nonbonded pdb=" OG1 THR C 52 " pdb="MG MG C 703 " model vdw 1.929 2.170 nonbonded pdb=" O2G AGS B 702 " pdb="MG MG B 703 " model vdw 1.946 2.170 nonbonded pdb=" O2G AGS D 702 " pdb="MG MG D 703 " model vdw 1.969 2.170 nonbonded pdb=" OG1 THR D 52 " pdb="MG MG D 703 " model vdw 1.984 2.170 nonbonded pdb=" OG1 THR B 52 " pdb="MG MG B 703 " model vdw 1.997 2.170 ... (remaining 177201 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 'B' and (resid 2 through 361 or resid 701 through 703)) selection = (chain 'C' and (resid 2 through 361 or resid 701 through 703)) selection = chain 'D' } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 1 through 365) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.770 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 22087 Z= 0.258 Angle : 0.630 14.273 30330 Z= 0.380 Chirality : 0.040 0.277 3489 Planarity : 0.004 0.039 3649 Dihedral : 17.174 162.023 8537 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.00 (0.17), residues: 2515 helix: 1.92 (0.15), residues: 1272 sheet: 1.71 (0.24), residues: 433 loop : 0.22 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 158 TYR 0.009 0.001 TYR G 284 PHE 0.010 0.001 PHE G 230 TRP 0.017 0.001 TRP B 10 HIS 0.007 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.26 (22071) covalent geometry : angle 0.60982 / 0.38 (30306) hydrogen bonds : bond 0.13526 / 9.42 ( 1234) hydrogen bonds : angle 4.88839 / 3.60 ( 3431) metal coordination : bond 0.00531 / 0.25 ( 16) metal coordination : angle 5.63135 / 3.40 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 GLU cc_start: 0.7459 (pm20) cc_final: 0.7252 (pm20) REVERT: C 137 ASN cc_start: 0.8598 (m-40) cc_final: 0.8377 (m110) REVERT: D 110 ASN cc_start: 0.8621 (t0) cc_final: 0.8326 (t0) REVERT: F 211 ASP cc_start: 0.8061 (t0) cc_final: 0.7846 (t0) REVERT: F 310 TYR cc_start: 0.7881 (t80) cc_final: 0.7672 (t80) REVERT: F 362 MET cc_start: 0.8662 (mmm) cc_final: 0.8284 (mmt) REVERT: G 2 LYS cc_start: 0.8677 (ttmm) cc_final: 0.8351 (ttmm) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.8983 time to fit residues: 408.2843 Evaluate side-chains 314 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0050 chunk 111 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN A 136 GLN A 167 ASN A 333 HIS B 160 GLN B 172 GLN B 186 GLN C 231 GLN D 78 ASN D 137 ASN E 51 GLN F 149 GLN F 329 ASN G 91 GLN G 175 HIS G 186 GLN G 265 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.061179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2337 r_free = 0.2337 target = 0.044130 restraints weight = 35982.619| |-----------------------------------------------------------------------------| r_work (start): 0.2327 rms_B_bonded: 1.05 r_work: 0.2231 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2139 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22087 Z= 0.144 Angle : 0.609 20.943 30330 Z= 0.311 Chirality : 0.040 0.326 3489 Planarity : 0.005 0.050 3649 Dihedral : 17.493 162.159 3741 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.37 % Allowed : 10.12 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.10 (0.17), residues: 2515 helix: 2.01 (0.15), residues: 1301 sheet: 1.79 (0.23), residues: 427 loop : 0.18 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 56 TYR 0.029 0.001 TYR C 3 PHE 0.014 0.001 PHE F 319 TRP 0.016 0.001 TRP B 10 HIS 0.006 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (22071) covalent geometry : angle 0.57295 / 0.31 (30306) hydrogen bonds : bond 0.04617 / 3.17 ( 1234) hydrogen bonds : angle 4.08333 / 2.99 ( 3431) metal coordination : bond 0.00776 / 0.34 ( 16) metal coordination : angle 7.34851 / 4.18 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 329 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8794 (mp) REVERT: B 3 TYR cc_start: 0.8538 (m-80) cc_final: 0.8262 (m-80) REVERT: B 247 ASP cc_start: 0.8323 (p0) cc_final: 0.8056 (p0) REVERT: B 285 MET cc_start: 0.8883 (mtp) cc_final: 0.8469 (ttm) REVERT: D 137 ASN cc_start: 0.8807 (m110) cc_final: 0.8606 (m-40) REVERT: D 333 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8640 (tt) REVERT: F 53 MET cc_start: 0.8850 (mtt) cc_final: 0.8555 (mtt) REVERT: F 211 ASP cc_start: 0.8079 (t0) cc_final: 0.7837 (t0) REVERT: F 315 MET cc_start: 0.8753 (ppp) cc_final: 0.8528 (ppp) REVERT: G 98 LEU cc_start: 0.8511 (mt) cc_final: 0.8173 (mt) outliers start: 29 outliers final: 9 residues processed: 344 average time/residue: 0.8451 time to fit residues: 321.7657 Evaluate side-chains 314 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 303 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 151 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 255 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN A 167 ASN A 333 HIS B 160 GLN B 198 HIS C 330 GLN D 110 ASN E 126 ASN F 217 GLN F 251 ASN G 61 GLN G 143 GLN G 186 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.058995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2275 r_free = 0.2275 target = 0.041848 restraints weight = 36140.417| |-----------------------------------------------------------------------------| r_work (start): 0.2266 rms_B_bonded: 1.09 r_work: 0.2169 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2076 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 22087 Z= 0.213 Angle : 0.679 27.119 30330 Z= 0.339 Chirality : 0.042 0.330 3489 Planarity : 0.005 0.055 3649 Dihedral : 17.557 163.232 3741 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.55 % Allowed : 11.54 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.91 (0.17), residues: 2515 helix: 1.86 (0.14), residues: 1302 sheet: 1.75 (0.24), residues: 423 loop : 0.05 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 36 TYR 0.040 0.002 TYR C 3 PHE 0.015 0.002 PHE F 3 TRP 0.014 0.002 TRP C 10 HIS 0.010 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (22071) covalent geometry : angle 0.63117 / 0.34 (30306) hydrogen bonds : bond 0.04875 / 3.36 ( 1234) hydrogen bonds : angle 4.01143 / 2.93 ( 3431) metal coordination : bond 0.01449 / 0.72 ( 16) metal coordination : angle 8.92462 / 5.02 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 319 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8796 (mp) REVERT: A 130 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8645 (mm) REVERT: A 149 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8329 (ptm-80) REVERT: A 225 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8373 (mmpt) REVERT: B 36 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8291 (mtm180) REVERT: D 263 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.7886 (ttt180) REVERT: D 330 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7895 (tp40) REVERT: D 333 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8743 (tt) REVERT: E 99 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8460 (mtpt) REVERT: F 53 MET cc_start: 0.8909 (mtt) cc_final: 0.8632 (mtt) REVERT: F 206 MET cc_start: 0.9121 (ttp) cc_final: 0.8837 (ttp) REVERT: F 211 ASP cc_start: 0.8140 (t0) cc_final: 0.7901 (t0) REVERT: F 335 ASN cc_start: 0.7687 (m-40) cc_final: 0.7437 (m110) outliers start: 54 outliers final: 18 residues processed: 344 average time/residue: 0.8082 time to fit residues: 308.8529 Evaluate side-chains 332 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 305 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 338 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 112 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 155 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 249 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 160 GLN B 192 ASN C 39 HIS C 137 ASN C 330 GLN D 78 ASN D 110 ASN D 137 ASN D 186 GLN E 126 ASN E 287 GLN F 149 GLN F 222 ASN F 251 ASN G 186 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.060723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2322 r_free = 0.2322 target = 0.043518 restraints weight = 35828.725| |-----------------------------------------------------------------------------| r_work (start): 0.2313 rms_B_bonded: 1.04 r_work: 0.2218 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2127 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22087 Z= 0.134 Angle : 0.598 24.332 30330 Z= 0.300 Chirality : 0.039 0.324 3489 Planarity : 0.005 0.055 3649 Dihedral : 17.472 163.571 3741 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.36 % Allowed : 12.53 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.05 (0.17), residues: 2515 helix: 2.06 (0.15), residues: 1304 sheet: 1.56 (0.24), residues: 422 loop : 0.12 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 282 TYR 0.028 0.001 TYR C 3 PHE 0.013 0.001 PHE F 3 TRP 0.017 0.001 TRP B 10 HIS 0.005 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (22071) covalent geometry : angle 0.55292 / 0.30 (30306) hydrogen bonds : bond 0.03959 / 2.69 ( 1234) hydrogen bonds : angle 3.82294 / 2.79 ( 3431) metal coordination : bond 0.00830 / 0.38 ( 16) metal coordination : angle 8.07776 / 4.51 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 320 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 17 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8790 (mp) REVERT: A 130 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8658 (mm) REVERT: A 149 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8309 (ptm-80) REVERT: A 225 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8465 (mmpt) REVERT: B 36 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8251 (mtm180) REVERT: B 247 ASP cc_start: 0.8242 (p0) cc_final: 0.8018 (p0) REVERT: C 1 MET cc_start: 0.4918 (OUTLIER) cc_final: 0.4665 (ppp) REVERT: C 337 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8501 (mttp) REVERT: D 148 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7833 (tp30) REVERT: D 263 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7886 (ttt180) REVERT: D 277 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.7878 (tm-30) REVERT: D 333 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8668 (tt) REVERT: E 99 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8460 (mtpt) REVERT: F 53 MET cc_start: 0.8821 (mtt) cc_final: 0.8583 (mtt) REVERT: F 211 ASP cc_start: 0.8033 (t0) cc_final: 0.7804 (t0) REVERT: F 335 ASN cc_start: 0.7567 (m-40) cc_final: 0.7310 (m110) outliers start: 50 outliers final: 16 residues processed: 344 average time/residue: 0.8074 time to fit residues: 307.8792 Evaluate side-chains 334 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 307 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 337 LYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 151 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 49 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 chunk 221 optimal weight: 0.2980 chunk 231 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 161 optimal weight: 1.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN A 333 HIS B 160 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN E 126 ASN E 287 GLN F 149 GLN F 251 ASN G 186 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.060565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2319 r_free = 0.2319 target = 0.043407 restraints weight = 35772.382| |-----------------------------------------------------------------------------| r_work (start): 0.2310 rms_B_bonded: 1.06 r_work: 0.2217 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2125 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 22087 Z= 0.145 Angle : 0.612 24.097 30330 Z= 0.305 Chirality : 0.039 0.316 3489 Planarity : 0.005 0.055 3649 Dihedral : 17.439 164.054 3741 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.41 % Allowed : 13.48 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.17), residues: 2515 helix: 2.08 (0.15), residues: 1305 sheet: 1.43 (0.24), residues: 427 loop : 0.17 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 36 TYR 0.025 0.001 TYR C 3 PHE 0.027 0.001 PHE G 230 TRP 0.015 0.001 TRP B 10 HIS 0.005 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (22071) covalent geometry : angle 0.56445 / 0.30 (30306) hydrogen bonds : bond 0.03996 / 2.73 ( 1234) hydrogen bonds : angle 3.81393 / 2.79 ( 3431) metal coordination : bond 0.01056 / 0.49 ( 16) metal coordination : angle 8.42854 / 5.23 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 321 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 17 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8768 (mp) REVERT: A 130 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8663 (mm) REVERT: A 149 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8336 (ptm-80) REVERT: A 225 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8463 (mmpt) REVERT: B 36 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8258 (mtm180) REVERT: B 247 ASP cc_start: 0.8246 (p0) cc_final: 0.8013 (p0) REVERT: B 285 MET cc_start: 0.8899 (mtp) cc_final: 0.8405 (ttm) REVERT: C 337 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8674 (mttp) REVERT: D 148 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7870 (tp30) REVERT: D 263 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7849 (ttt180) REVERT: D 277 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: D 330 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7932 (tp40) REVERT: D 333 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8675 (tt) REVERT: E 99 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8477 (mtpt) REVERT: F 53 MET cc_start: 0.8852 (mtt) cc_final: 0.8598 (mtt) REVERT: F 211 ASP cc_start: 0.8085 (t0) cc_final: 0.7847 (t0) REVERT: F 335 ASN cc_start: 0.7554 (m-40) cc_final: 0.7292 (m110) outliers start: 51 outliers final: 21 residues processed: 347 average time/residue: 0.7950 time to fit residues: 305.5905 Evaluate side-chains 337 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 305 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 337 LYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 204 MET Chi-restraints excluded: chain G residue 338 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 202 optimal weight: 0.0670 chunk 136 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 chunk 86 optimal weight: 0.5980 chunk 215 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 222 optimal weight: 0.0870 chunk 168 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN A 333 HIS B 160 GLN D 39 HIS D 78 ASN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN E 126 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN F 251 ASN G 186 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.061136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2334 r_free = 0.2334 target = 0.043983 restraints weight = 36237.620| |-----------------------------------------------------------------------------| r_work (start): 0.2325 rms_B_bonded: 1.05 r_work: 0.2233 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2143 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22087 Z= 0.128 Angle : 0.592 22.797 30330 Z= 0.297 Chirality : 0.039 0.306 3489 Planarity : 0.005 0.055 3649 Dihedral : 17.389 164.363 3741 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.41 % Allowed : 14.42 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.15 (0.17), residues: 2515 helix: 2.17 (0.15), residues: 1302 sheet: 1.60 (0.24), residues: 414 loop : 0.15 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 246 TYR 0.021 0.001 TYR C 3 PHE 0.035 0.001 PHE G 230 TRP 0.015 0.001 TRP B 10 HIS 0.005 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (22071) covalent geometry : angle 0.55155 / 0.29 (30306) hydrogen bonds : bond 0.03748 / 2.55 ( 1234) hydrogen bonds : angle 3.74022 / 2.73 ( 3431) metal coordination : bond 0.00850 / 0.39 ( 16) metal coordination : angle 7.71062 / 4.76 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 321 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 17 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8772 (mp) REVERT: A 39 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.7954 (mtt180) REVERT: A 130 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8666 (mm) REVERT: A 149 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8286 (ptm-80) REVERT: A 225 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8514 (mmpt) REVERT: B 36 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8232 (mtm180) REVERT: B 247 ASP cc_start: 0.8223 (p0) cc_final: 0.8012 (p0) REVERT: B 285 MET cc_start: 0.8897 (mtp) cc_final: 0.8354 (ttm) REVERT: C 337 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8653 (mttp) REVERT: D 148 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7888 (tp30) REVERT: D 263 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7879 (ttt180) REVERT: D 277 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: D 330 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7923 (tp40) REVERT: D 333 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8643 (tt) REVERT: E 99 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8464 (mtpt) REVERT: F 53 MET cc_start: 0.8844 (mtt) cc_final: 0.8595 (mtt) REVERT: F 211 ASP cc_start: 0.8103 (t0) cc_final: 0.7864 (t0) REVERT: F 335 ASN cc_start: 0.7435 (m-40) cc_final: 0.7178 (m110) REVERT: G 215 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8032 (ttm170) outliers start: 51 outliers final: 15 residues processed: 348 average time/residue: 0.8062 time to fit residues: 309.7955 Evaluate side-chains 343 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 315 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 337 LYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 215 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 42 optimal weight: 0.0570 chunk 142 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 170 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 179 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN A 167 ASN A 333 HIS B 160 GLN B 326 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN F 251 ASN G 16 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.061106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2333 r_free = 0.2333 target = 0.043932 restraints weight = 36036.175| |-----------------------------------------------------------------------------| r_work (start): 0.2324 rms_B_bonded: 1.05 r_work: 0.2231 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2140 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 22087 Z= 0.134 Angle : 0.593 22.351 30330 Z= 0.299 Chirality : 0.039 0.293 3489 Planarity : 0.005 0.059 3649 Dihedral : 17.340 163.783 3741 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.88 % Allowed : 14.18 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.14 (0.17), residues: 2515 helix: 2.17 (0.15), residues: 1302 sheet: 1.36 (0.23), residues: 428 loop : 0.22 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG D 36 TYR 0.020 0.001 TYR C 3 PHE 0.037 0.001 PHE G 230 TRP 0.013 0.001 TRP B 10 HIS 0.005 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (22071) covalent geometry : angle 0.55659 / 0.30 (30306) hydrogen bonds : bond 0.03784 / 2.58 ( 1234) hydrogen bonds : angle 3.72641 / 2.73 ( 3431) metal coordination : bond 0.00757 / 0.35 ( 16) metal coordination : angle 7.30756 / 4.53 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 323 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 17 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8766 (mp) REVERT: A 39 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.7951 (mtt180) REVERT: A 130 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8662 (mm) REVERT: A 149 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8297 (ptm-80) REVERT: A 225 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8460 (mmpt) REVERT: B 36 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8223 (mtm180) REVERT: B 247 ASP cc_start: 0.8203 (p0) cc_final: 0.7982 (p0) REVERT: B 285 MET cc_start: 0.8911 (mtp) cc_final: 0.8456 (ttm) REVERT: C 337 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8651 (mttp) REVERT: D 148 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7902 (tp30) REVERT: D 215 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8015 (ttm170) REVERT: D 263 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7836 (ttt180) REVERT: D 277 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: D 330 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.7924 (tp40) REVERT: D 333 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8648 (tt) REVERT: E 99 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8458 (mtpt) REVERT: F 53 MET cc_start: 0.8873 (mtt) cc_final: 0.8641 (mtt) REVERT: F 211 ASP cc_start: 0.8102 (t0) cc_final: 0.7861 (t0) REVERT: F 279 ARG cc_start: 0.8078 (mpp80) cc_final: 0.7722 (mpp80) REVERT: F 335 ASN cc_start: 0.7436 (m-40) cc_final: 0.7147 (m-40) REVERT: G 215 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8036 (ttm170) REVERT: G 230 PHE cc_start: 0.7278 (m-80) cc_final: 0.6919 (m-80) outliers start: 61 outliers final: 24 residues processed: 357 average time/residue: 0.7432 time to fit residues: 294.0187 Evaluate side-chains 348 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 310 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 337 LYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 215 ARG Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 215 ARG Chi-restraints excluded: chain G residue 338 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 59 optimal weight: 0.6980 chunk 143 optimal weight: 0.0770 chunk 81 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 233 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS B 160 GLN D 78 ASN D 110 ASN E 287 GLN F 149 GLN F 251 ASN ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.061300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2338 r_free = 0.2338 target = 0.044113 restraints weight = 36147.051| |-----------------------------------------------------------------------------| r_work (start): 0.2329 rms_B_bonded: 1.05 r_work: 0.2237 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2147 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22087 Z= 0.132 Angle : 0.592 15.124 30330 Z= 0.300 Chirality : 0.039 0.280 3489 Planarity : 0.005 0.061 3649 Dihedral : 17.298 162.749 3741 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.60 % Allowed : 14.85 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.16 (0.17), residues: 2515 helix: 2.18 (0.15), residues: 1302 sheet: 1.40 (0.24), residues: 423 loop : 0.24 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 246 TYR 0.016 0.001 TYR F 310 PHE 0.031 0.001 PHE G 230 TRP 0.014 0.001 TRP B 10 HIS 0.005 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (22071) covalent geometry : angle 0.55974 / 0.30 (30306) hydrogen bonds : bond 0.03723 / 2.53 ( 1234) hydrogen bonds : angle 3.72630 / 2.73 ( 3431) metal coordination : bond 0.00639 / 0.30 ( 16) metal coordination : angle 6.91828 / 4.72 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 312 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 17 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8764 (mp) REVERT: A 39 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.7947 (mtt180) REVERT: A 130 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8656 (mm) REVERT: A 225 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8478 (mmpt) REVERT: B 36 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8210 (mtm180) REVERT: B 247 ASP cc_start: 0.8149 (p0) cc_final: 0.7922 (p0) REVERT: B 285 MET cc_start: 0.8920 (mtp) cc_final: 0.8472 (ttm) REVERT: C 337 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8643 (mttp) REVERT: D 148 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7933 (tp30) REVERT: D 215 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8022 (ttm170) REVERT: D 263 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.7789 (ttt180) REVERT: D 277 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: D 330 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.7924 (tp40) REVERT: D 333 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8641 (tt) REVERT: D 347 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8706 (ttp) REVERT: E 99 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8459 (mtpt) REVERT: F 53 MET cc_start: 0.8866 (mtt) cc_final: 0.8631 (mtt) REVERT: F 211 ASP cc_start: 0.8073 (t0) cc_final: 0.7843 (t0) REVERT: F 279 ARG cc_start: 0.8089 (mpp80) cc_final: 0.7743 (mpp80) REVERT: F 310 TYR cc_start: 0.7911 (t80) cc_final: 0.7488 (t80) REVERT: F 332 LYS cc_start: 0.8572 (ptpt) cc_final: 0.8355 (ptpp) REVERT: G 215 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8028 (ttm170) outliers start: 55 outliers final: 21 residues processed: 342 average time/residue: 0.7696 time to fit residues: 291.1514 Evaluate side-chains 341 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 306 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 337 LYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 215 ARG Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 215 ARG Chi-restraints excluded: chain G residue 338 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 93 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 243 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN A 333 HIS B 160 GLN D 137 ASN E 246 HIS E 287 GLN F 16 GLN F 149 GLN F 251 ASN ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.060508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2316 r_free = 0.2316 target = 0.043307 restraints weight = 35850.077| |-----------------------------------------------------------------------------| r_work (start): 0.2307 rms_B_bonded: 1.07 r_work: 0.2214 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2123 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 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 : 0.004 0.080 22087 Z= 0.161 Angle : 0.629 13.636 30330 Z= 0.319 Chirality : 0.040 0.288 3489 Planarity : 0.005 0.064 3649 Dihedral : 17.309 161.485 3741 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.32 % Allowed : 15.32 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.05 (0.17), residues: 2515 helix: 2.07 (0.15), residues: 1309 sheet: 1.34 (0.23), residues: 427 loop : 0.23 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 149 TYR 0.014 0.002 TYR C 3 PHE 0.033 0.002 PHE G 230 TRP 0.012 0.001 TRP B 10 HIS 0.006 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (22071) covalent geometry : angle 0.59934 / 0.32 (30306) hydrogen bonds : bond 0.04048 / 2.75 ( 1234) hydrogen bonds : angle 3.78694 / 2.77 ( 3431) metal coordination : bond 0.00815 / 0.39 ( 16) metal coordination : angle 6.85839 / 4.61 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 307 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 17 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8768 (mp) REVERT: A 39 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.7923 (mtt180) REVERT: A 196 LYS cc_start: 0.8821 (mmmm) cc_final: 0.8575 (mmpt) REVERT: A 225 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8429 (mmpt) REVERT: B 36 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8232 (mtm180) REVERT: B 247 ASP cc_start: 0.8153 (p0) cc_final: 0.7945 (p0) REVERT: C 337 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8707 (mttp) REVERT: D 148 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7962 (tp30) REVERT: D 263 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.7854 (ttt180) REVERT: D 277 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: D 330 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7922 (tp40) REVERT: D 333 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8691 (tt) REVERT: E 99 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8483 (mtpt) REVERT: E 253 MET cc_start: 0.8763 (ttm) cc_final: 0.8385 (ttp) REVERT: F 16 GLN cc_start: 0.7372 (mt0) cc_final: 0.7151 (mt0) REVERT: F 53 MET cc_start: 0.8911 (mtt) cc_final: 0.8696 (mtt) REVERT: F 206 MET cc_start: 0.8796 (ttt) cc_final: 0.8348 (ttm) REVERT: F 211 ASP cc_start: 0.8087 (t0) cc_final: 0.7859 (t0) REVERT: F 279 ARG cc_start: 0.8111 (mpp80) cc_final: 0.7755 (mpp80) REVERT: F 310 TYR cc_start: 0.7909 (t80) cc_final: 0.7445 (t80) REVERT: G 215 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8045 (ttm170) outliers start: 49 outliers final: 27 residues processed: 334 average time/residue: 0.8296 time to fit residues: 306.9087 Evaluate side-chains 341 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 303 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 337 LYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 146 ARG Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 215 ARG Chi-restraints excluded: chain G residue 338 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 181 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS B 160 GLN D 78 ASN E 246 HIS ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN G 16 GLN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.060209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2307 r_free = 0.2307 target = 0.042997 restraints weight = 36072.621| |-----------------------------------------------------------------------------| r_work (start): 0.2299 rms_B_bonded: 1.04 r_work: 0.2207 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2115 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 22087 Z= 0.164 Angle : 0.634 13.626 30330 Z= 0.321 Chirality : 0.040 0.284 3489 Planarity : 0.005 0.067 3649 Dihedral : 17.320 162.100 3741 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.22 % Allowed : 15.60 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.00 (0.17), residues: 2515 helix: 2.03 (0.15), residues: 1309 sheet: 1.30 (0.23), residues: 431 loop : 0.20 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 149 TYR 0.023 0.002 TYR F 284 PHE 0.019 0.002 PHE G 3 TRP 0.013 0.001 TRP B 10 HIS 0.006 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (22071) covalent geometry : angle 0.60419 / 0.32 (30306) hydrogen bonds : bond 0.04094 / 2.78 ( 1234) hydrogen bonds : angle 3.80011 / 2.78 ( 3431) metal coordination : bond 0.00798 / 0.38 ( 16) metal coordination : angle 6.88822 / 4.59 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5030 Ramachandran restraints generated. 2515 Oldfield, 0 Emsley, 2515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 308 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 17 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8768 (mp) REVERT: A 39 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.7856 (mtt180) REVERT: A 225 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8431 (mmpt) REVERT: B 36 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8245 (mtm180) REVERT: B 247 ASP cc_start: 0.8150 (p0) cc_final: 0.7930 (p0) REVERT: C 337 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8690 (mttp) REVERT: D 148 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7991 (tp30) REVERT: D 215 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.7995 (ttm170) REVERT: D 263 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.7807 (ttt180) REVERT: D 277 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: D 330 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.7923 (tp40) REVERT: D 333 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8718 (tt) REVERT: E 99 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8494 (mtpt) REVERT: F 16 GLN cc_start: 0.7367 (mt0) cc_final: 0.7158 (mt0) REVERT: F 53 MET cc_start: 0.8908 (mtt) cc_final: 0.8687 (mtt) REVERT: F 211 ASP cc_start: 0.8093 (t0) cc_final: 0.7871 (t0) REVERT: F 254 LYS cc_start: 0.8709 (mtmm) cc_final: 0.8416 (mttm) REVERT: F 279 ARG cc_start: 0.8132 (mpp80) cc_final: 0.7741 (mpp80) REVERT: G 16 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7834 (pm20) REVERT: G 91 GLN cc_start: 0.7460 (pt0) cc_final: 0.7230 (pt0) REVERT: G 215 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8050 (ttm170) outliers start: 47 outliers final: 27 residues processed: 339 average time/residue: 0.7932 time to fit residues: 297.4562 Evaluate side-chains 344 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 304 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 337 LYS Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 215 ARG Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 347 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 215 ARG Chi-restraints excluded: chain G residue 338 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 1 optimal weight: 0.6980 chunk 248 optimal weight: 9.9990 chunk 195 optimal weight: 0.3980 chunk 138 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 252 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN A 333 HIS B 160 GLN ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 HIS ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.060216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2308 r_free = 0.2308 target = 0.043060 restraints weight = 35834.701| |-----------------------------------------------------------------------------| r_work (start): 0.2299 rms_B_bonded: 1.07 r_work: 0.2206 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2116 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 22087 Z= 0.195 Angle : 0.791 59.199 30330 Z= 0.430 Chirality : 0.040 0.371 3489 Planarity : 0.005 0.063 3649 Dihedral : 17.319 162.093 3741 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.13 % Allowed : 15.93 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.00 (0.17), residues: 2515 helix: 2.03 (0.15), residues: 1309 sheet: 1.29 (0.23), residues: 431 loop : 0.20 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 246 TYR 0.022 0.002 TYR F 284 PHE 0.019 0.001 PHE G 3 TRP 0.013 0.001 TRP B 10 HIS 0.006 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (22071) covalent geometry : angle 0.76760 / 0.43 (30306) hydrogen bonds : bond 0.04080 / 2.77 ( 1234) hydrogen bonds : angle 3.79355 / 2.77 ( 3431) metal coordination : bond 0.00766 / 0.37 ( 16) metal coordination : angle 6.88173 / 4.58 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8185.69 seconds wall clock time: 139 minutes 55.77 seconds (8395.77 seconds total)