Starting phenix.real_space_refine on Sun Sep 13 05:19:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sh2_25122/09_2026/7sh2_25122.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sh2_25122/09_2026/7sh2_25122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7sh2_25122/09_2026/7sh2_25122.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sh2_25122/09_2026/7sh2_25122.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sh2_25122/09_2026/7sh2_25122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sh2_25122/09_2026/7sh2_25122.map" model { file = "/net/cci-nas-00/data/ceres_data/7sh2_25122/09_2026/7sh2_25122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sh2_25122/09_2026/7sh2_25122.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 4 5.21 5 S 113 5.16 5 C 13174 2.51 5 N 3597 2.21 5 O 4009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20933 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3309 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 389} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2489 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "C" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2569 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2617 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2692 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "F" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2178 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 8, 'TRANS': 260} Chain breaks: 6 Chain: "G" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2313 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 4, 'TRANS': 287} Chain breaks: 1 Chain: "H" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2145 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 5 Chain: "P" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.23, per 1000 atoms: 0.20 Number of scatterers: 20933 At special positions: 0 Unit cell: (135.792, 125.856, 142.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 113 16.00 P 36 15.00 Mg 4 11.99 O 4009 8.00 N 3597 7.00 C 13174 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: 1.67 Conformation dependent library (CDL) restraints added in 734.6 milliseconds 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4868 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 18 sheets defined 51.7% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 81 through 97 removed outlier: 3.530A pdb=" N LEU A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 127 removed outlier: 3.766A pdb=" N ILE A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 163 through 175 removed outlier: 3.529A pdb=" N TYR A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 210 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 284 through 291 removed outlier: 3.572A pdb=" N LYS A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 308 removed outlier: 3.530A pdb=" N THR A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 367 removed outlier: 3.709A pdb=" N MET A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'A' and resid 376 through 384 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 393 through 409 removed outlier: 3.658A pdb=" N ALA A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 432 Processing helix chain 'A' and resid 446 through 471 Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.529A pdb=" N LEU A 490 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.659A pdb=" N TYR B 15 " --> pdb=" O TRP B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 69 through 73 removed outlier: 4.229A pdb=" N ALA B 72 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 73 " --> pdb=" O SER B 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 73' Processing helix chain 'B' and resid 87 through 98 Processing helix chain 'B' and resid 120 through 134 Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.602A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 260 removed outlier: 4.234A pdb=" N LYS B 258 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 302 Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.717A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 59 through 71 Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.929A pdb=" N VAL C 79 " --> pdb=" O TYR C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 103 removed outlier: 3.584A pdb=" N THR C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.508A pdb=" N GLU C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.538A pdb=" N LEU C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 4.098A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 219 Processing helix chain 'C' and resid 228 through 237 removed outlier: 3.603A pdb=" N ILE C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 256 through 270 removed outlier: 3.891A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.813A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 313 Processing helix chain 'C' and resid 315 through 332 Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 43 through 54 removed outlier: 3.971A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 102 through 114 Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 160 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 193 through 208 removed outlier: 5.294A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.514A pdb=" N GLY D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.548A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 Processing helix chain 'D' and resid 279 through 294 Processing helix chain 'D' and resid 296 through 311 removed outlier: 3.745A pdb=" N VAL D 300 " --> pdb=" O SER D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.585A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.200A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 103 through 118 removed outlier: 4.484A pdb=" N ILE E 107 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 161 removed outlier: 3.809A pdb=" N ALA E 153 " --> pdb=" O ASP E 149 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 185 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.666A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 291 Processing helix chain 'E' and resid 295 through 309 removed outlier: 3.506A pdb=" N ILE E 299 " --> pdb=" O PRO E 295 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP E 309 " --> pdb=" O PHE E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 335 Processing helix chain 'E' and resid 338 through 354 removed outlier: 3.611A pdb=" N LEU E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP E 354 " --> pdb=" O MET E 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 30 removed outlier: 3.780A pdb=" N TYR F 16 " --> pdb=" O ALA F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 109 removed outlier: 3.506A pdb=" N SER F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 220 Processing helix chain 'F' and resid 239 through 256 removed outlier: 4.392A pdb=" N GLY F 243 " --> pdb=" O SER F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 422 Processing helix chain 'G' and resid 17 through 26 removed outlier: 4.335A pdb=" N ILE G 21 " --> pdb=" O HIS G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 33 removed outlier: 3.765A pdb=" N SER G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 96 removed outlier: 3.695A pdb=" N ILE G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET G 96 " --> pdb=" O SER G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 150 No H-bonds generated for 'chain 'G' and resid 148 through 150' Processing helix chain 'G' and resid 160 through 172 removed outlier: 4.298A pdb=" N GLU G 172 " --> pdb=" O LYS G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 249 removed outlier: 4.164A pdb=" N LYS G 247 " --> pdb=" O ASP G 243 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 329 removed outlier: 4.230A pdb=" N GLU G 323 " --> pdb=" O ALA G 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 27 Processing helix chain 'H' and resid 58 through 61 Processing helix chain 'H' and resid 67 through 71 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 98 through 103 removed outlier: 3.612A pdb=" N THR H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 209 Processing helix chain 'H' and resid 234 through 243 Processing helix chain 'H' and resid 245 through 249 removed outlier: 3.630A pdb=" N VAL H 248 " --> pdb=" O ASN H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 334 Processing helix chain 'H' and resid 334 through 339 removed outlier: 3.715A pdb=" N SER H 338 " --> pdb=" O THR H 334 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TRP H 339 " --> pdb=" O ILE H 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 334 through 339' Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 removed outlier: 5.787A pdb=" N THR A 149 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU A 105 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A 261 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 106 " --> pdb=" O LYS A 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 109 through 114 removed outlier: 6.127A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N MET B 45 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 82 removed outlier: 3.613A pdb=" N LEU C 80 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 147 " --> pdb=" O PHE C 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 93 through 95 removed outlier: 4.049A pdb=" N LEU D 93 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR D 64 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 69 through 70 removed outlier: 3.566A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU E 95 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER E 90 " --> pdb=" O HIS E 93 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS E 93 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE E 96 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU E 39 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 73 through 78 removed outlier: 4.085A pdb=" N ARG E 73 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG E 81 " --> pdb=" O THR E 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.372A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 78 through 81 removed outlier: 6.109A pdb=" N LEU F 79 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE F 6 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS F 4 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU F 5 " --> pdb=" O ILE F 121 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE F 121 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR F 120 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR F 159 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS F 122 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY F 157 " --> pdb=" O LYS F 122 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS F 203 " --> pdb=" O PHE F 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 34 through 35 Processing sheet with id=AB1, first strand: chain 'F' and resid 42 through 44 removed outlier: 4.047A pdb=" N THR F 43 " --> pdb=" O ILE F 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 231 through 232 removed outlier: 3.540A pdb=" N CYS F 438 " --> pdb=" O HIS F 434 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 231 through 232 removed outlier: 3.522A pdb=" N ASP F 445 " --> pdb=" O GLY F 462 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 263 through 266 removed outlier: 5.008A pdb=" N HIS F 291 " --> pdb=" O GLU G 131 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU G 131 " --> pdb=" O HIS F 291 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N CYS F 295 " --> pdb=" O SER G 127 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER G 127 " --> pdb=" O CYS F 295 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 80 through 84 removed outlier: 4.090A pdb=" N MET G 80 " --> pdb=" O ILE G 41 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE G 41 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU G 82 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL G 49 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN G 52 " --> pdb=" O ILE G 56 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET G 259 " --> pdb=" O PHE G 154 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N SER G 153 " --> pdb=" O PHE G 220 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL G 219 " --> pdb=" O ILE G 228 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 233 through 238 removed outlier: 3.657A pdb=" N ALA G 193 " --> pdb=" O TYR G 181 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE G 192 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL H 145 " --> pdb=" O LYS G 206 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR H 117 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE H 118 " --> pdb=" O THR H 6 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR H 6 " --> pdb=" O ILE H 118 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 233 through 238 removed outlier: 4.113A pdb=" N GLU G 177 " --> pdb=" O LYS G 197 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL H 145 " --> pdb=" O LYS G 206 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR H 117 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE H 118 " --> pdb=" O THR H 6 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR H 6 " --> pdb=" O ILE H 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 78 through 79 removed outlier: 3.625A pdb=" N GLN H 79 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU H 375 " --> pdb=" O ILE H 360 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN H 363 " --> pdb=" O ILE H 349 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE H 230 " --> pdb=" O SER H 350 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 283 through 285 removed outlier: 3.679A pdb=" N MET H 284 " --> pdb=" O ALA H 265 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU H 255 " --> pdb=" O SER H 262 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR H 264 " --> pdb=" O LYS H 253 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL H 252 " --> pdb=" O PHE H 324 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE H 324 " --> pdb=" O VAL H 252 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU H 254 " --> pdb=" O ILE H 322 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE H 322 " --> pdb=" O LEU H 254 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 3018 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.98 Time building geometry restraints manager: 2.20 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: 6866 1.36 - 1.51: 5506 1.51 - 1.66: 8790 1.66 - 1.80: 100 1.80 - 1.95: 70 Bond restraints: 21332 Sorted by residual: bond pdb=" C3' DA T 22 " pdb=" C2' DA T 22 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DC T 30 " pdb=" C2' DC T 30 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.77e+00 bond pdb=" C1' DC P 8 " pdb=" N1 DC P 8 " ideal model delta sigma weight residual 1.468 1.501 -0.033 1.40e-02 5.10e+03 5.67e+00 bond pdb=" C3' DA T 22 " pdb=" O3' DA T 22 " ideal model delta sigma weight residual 1.435 1.462 -0.027 1.30e-02 5.92e+03 4.18e+00 bond pdb=" C3' DT T 24 " pdb=" C2' DT T 24 " ideal model delta sigma weight residual 1.516 1.532 -0.016 8.00e-03 1.56e+04 4.17e+00 ... (remaining 21327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 28457 1.98 - 3.97: 382 3.97 - 5.95: 60 5.95 - 7.93: 17 7.93 - 9.92: 3 Bond angle restraints: 28919 Sorted by residual: angle pdb=" C SER E 79 " pdb=" CA SER E 79 " pdb=" CB SER E 79 " ideal model delta sigma weight residual 116.54 110.32 6.22 1.15e+00 7.56e-01 2.93e+01 angle pdb=" CA PRO F 48 " pdb=" N PRO F 48 " pdb=" CD PRO F 48 " ideal model delta sigma weight residual 112.00 105.04 6.96 1.40e+00 5.10e-01 2.47e+01 angle pdb=" N3 DT T 28 " pdb=" C4 DT T 28 " pdb=" O4 DT T 28 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" C ILE G 324 " pdb=" N GLU G 325 " pdb=" CA GLU G 325 " ideal model delta sigma weight residual 120.29 114.08 6.21 1.42e+00 4.96e-01 1.92e+01 angle pdb=" N3 DT T 32 " pdb=" C4 DT T 32 " pdb=" O4 DT T 32 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.76e+01 ... (remaining 28914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 12627 35.05 - 70.11: 304 70.11 - 105.16: 21 105.16 - 140.22: 2 140.22 - 175.27: 1 Dihedral angle restraints: 12955 sinusoidal: 5493 harmonic: 7462 Sorted by residual: dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual 300.00 177.99 122.01 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 57.22 -124.95 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C4' DA T 22 " pdb=" C3' DA T 22 " pdb=" O3' DA T 22 " pdb=" P DG T 23 " ideal model delta sinusoidal sigma weight residual -140.00 35.27 -175.27 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 12952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2520 0.043 - 0.085: 610 0.085 - 0.128: 199 0.128 - 0.170: 11 0.170 - 0.213: 6 Chirality restraints: 3346 Sorted by residual: chirality pdb=" CB ILE G 103 " pdb=" CA ILE G 103 " pdb=" CG1 ILE G 103 " pdb=" CG2 ILE G 103 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB ILE G 251 " pdb=" CA ILE G 251 " pdb=" CG1 ILE G 251 " pdb=" CG2 ILE G 251 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA THR F 47 " pdb=" N THR F 47 " pdb=" C THR F 47 " pdb=" CB THR F 47 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.89e-01 ... (remaining 3343 not shown) Planarity restraints: 3560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " -0.085 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO F 48 " 0.214 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 167 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO C 168 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 168 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 168 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 488 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO A 489 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 489 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 489 " 0.025 5.00e-02 4.00e+02 ... (remaining 3557 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 383 2.69 - 3.24: 19811 3.24 - 3.79: 33058 3.79 - 4.35: 42662 4.35 - 4.90: 71211 Nonbonded interactions: 167125 Sorted by model distance: nonbonded pdb=" O1B AGS B 401 " pdb="MG MG B 402 " model vdw 2.135 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.144 2.170 nonbonded pdb=" O3G AGS B 401 " pdb="MG MG B 402 " model vdw 2.169 2.170 nonbonded pdb=" O LEU G 326 " pdb=" OG1 THR G 330 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR F 92 " pdb=" OG1 THR F 218 " model vdw 2.202 3.040 ... (remaining 167120 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.960 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.330 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 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 : 0.002 0.060 21332 Z= 0.150 Angle : 0.572 9.916 28919 Z= 0.320 Chirality : 0.042 0.213 3346 Planarity : 0.004 0.124 3560 Dihedral : 15.093 175.269 8087 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.04 % Allowed : 0.52 % Favored : 99.43 % 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: 0.45 (0.17), residues: 2497 helix: 1.46 (0.15), residues: 1225 sheet: 0.27 (0.27), residues: 440 loop : -1.43 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 36 TYR 0.015 0.001 TYR E 324 PHE 0.023 0.001 PHE F 205 TRP 0.026 0.001 TRP E 259 HIS 0.004 0.001 HIS F 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.15 (21332) covalent geometry : angle 0.57158 / 0.32 (28919) hydrogen bonds : bond 0.16560 / 10.92 ( 1019) hydrogen bonds : angle 6.54763 / 4.74 ( 3018) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 289 time to evaluate : 0.822 Fit side-chains REVERT: A 168 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7812 (tp30) REVERT: A 307 GLU cc_start: 0.7134 (tp30) cc_final: 0.6829 (tp30) REVERT: C 245 LYS cc_start: 0.7448 (tptt) cc_final: 0.6955 (mtmm) REVERT: D 80 LYS cc_start: 0.7291 (tppt) cc_final: 0.6384 (tmtt) REVERT: F 14 ASP cc_start: 0.6320 (m-30) cc_final: 0.5925 (m-30) REVERT: H 148 TYR cc_start: 0.5798 (m-80) cc_final: 0.5591 (m-80) REVERT: H 371 LEU cc_start: 0.5549 (mt) cc_final: 0.5319 (mt) outliers start: 1 outliers final: 0 residues processed: 290 average time/residue: 0.1268 time to fit residues: 60.5377 Evaluate side-chains 213 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.0970 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 GLN B 35 GLN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS D 313 ASN E 164 ASN F 463 GLN G 9 ASN G 54 HIS H 37 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.195006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.160914 restraints weight = 29491.075| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.42 r_work: 0.4002 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21332 Z= 0.179 Angle : 0.607 8.384 28919 Z= 0.319 Chirality : 0.043 0.201 3346 Planarity : 0.004 0.046 3560 Dihedral : 11.399 173.417 3012 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.96 % Allowed : 8.70 % Favored : 90.34 % 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: 0.50 (0.18), residues: 2497 helix: 1.46 (0.15), residues: 1227 sheet: 0.26 (0.27), residues: 436 loop : -1.34 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 332 TYR 0.022 0.001 TYR A 242 PHE 0.020 0.002 PHE G 40 TRP 0.012 0.002 TRP E 259 HIS 0.008 0.001 HIS E 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (21332) covalent geometry : angle 0.60732 / 0.32 (28919) hydrogen bonds : bond 0.04401 / 2.97 ( 1019) hydrogen bonds : angle 5.00826 / 3.60 ( 3018) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 256 time to evaluate : 0.766 Fit side-chains REVERT: A 168 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7947 (tp30) REVERT: A 307 GLU cc_start: 0.7260 (tp30) cc_final: 0.6873 (tp30) REVERT: D 80 LYS cc_start: 0.7665 (tppt) cc_final: 0.6776 (tmtt) REVERT: F 14 ASP cc_start: 0.7042 (m-30) cc_final: 0.6587 (m-30) REVERT: G 153 SER cc_start: 0.8399 (t) cc_final: 0.8069 (m) REVERT: G 259 MET cc_start: 0.5364 (ptp) cc_final: 0.4786 (ttt) REVERT: H 44 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.5050 (tpt) REVERT: H 253 LYS cc_start: 0.6337 (tptp) cc_final: 0.6083 (tptt) outliers start: 22 outliers final: 14 residues processed: 270 average time/residue: 0.1387 time to fit residues: 60.1498 Evaluate side-chains 236 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 221 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 54 HIS Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain H residue 44 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 16 optimal weight: 5.9990 chunk 174 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 251 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 218 optimal weight: 9.9990 chunk 201 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 ASN B 35 GLN B 64 HIS ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS D 196 ASN E 93 HIS E 164 ASN F 226 ASN G 9 ASN G 54 HIS H 37 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.192541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.157760 restraints weight = 29307.391| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 2.23 r_work: 0.3978 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21332 Z= 0.145 Angle : 0.554 7.679 28919 Z= 0.288 Chirality : 0.042 0.203 3346 Planarity : 0.004 0.047 3560 Dihedral : 11.415 172.789 3012 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.65 % Allowed : 10.84 % Favored : 87.51 % 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: 0.54 (0.18), residues: 2497 helix: 1.56 (0.15), residues: 1218 sheet: 0.21 (0.26), residues: 436 loop : -1.37 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 20 TYR 0.033 0.001 TYR B 71 PHE 0.017 0.001 PHE F 246 TRP 0.015 0.001 TRP E 259 HIS 0.005 0.001 HIS E 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (21332) covalent geometry : angle 0.55416 / 0.29 (28919) hydrogen bonds : bond 0.04010 / 2.71 ( 1019) hydrogen bonds : angle 4.72005 / 3.38 ( 3018) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 233 time to evaluate : 0.798 Fit side-chains REVERT: A 168 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7963 (tp30) REVERT: A 307 GLU cc_start: 0.7452 (tp30) cc_final: 0.7060 (tp30) REVERT: E 54 MET cc_start: 0.8555 (mmm) cc_final: 0.8350 (mmm) REVERT: F 14 ASP cc_start: 0.7166 (m-30) cc_final: 0.6757 (m-30) REVERT: F 23 ILE cc_start: 0.7429 (mm) cc_final: 0.6986 (mm) REVERT: G 153 SER cc_start: 0.8498 (t) cc_final: 0.8254 (m) REVERT: G 325 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7939 (pm20) REVERT: H 148 TYR cc_start: 0.6188 (m-80) cc_final: 0.5614 (m-80) REVERT: H 253 LYS cc_start: 0.6217 (tptp) cc_final: 0.5938 (tptt) outliers start: 38 outliers final: 25 residues processed: 258 average time/residue: 0.1360 time to fit residues: 56.1001 Evaluate side-chains 236 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 247 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain G residue 54 HIS Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 325 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 23 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 74 optimal weight: 0.0570 chunk 147 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 ASN B 35 GLN D 96 ASN D 124 HIS E 164 ASN H 37 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.193223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.159094 restraints weight = 29178.928| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.49 r_work: 0.3973 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21332 Z= 0.114 Angle : 0.525 8.508 28919 Z= 0.271 Chirality : 0.040 0.205 3346 Planarity : 0.003 0.046 3560 Dihedral : 11.385 172.095 3012 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.45 % Favored : 95.51 % Rotamer: Outliers : 1.74 % Allowed : 11.92 % Favored : 86.34 % 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: 0.68 (0.18), residues: 2497 helix: 1.72 (0.15), residues: 1218 sheet: 0.22 (0.27), residues: 431 loop : -1.32 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 20 TYR 0.024 0.001 TYR B 71 PHE 0.020 0.001 PHE G 202 TRP 0.019 0.001 TRP E 259 HIS 0.006 0.001 HIS G 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (21332) covalent geometry : angle 0.52501 / 0.27 (28919) hydrogen bonds : bond 0.03458 / 2.34 ( 1019) hydrogen bonds : angle 4.47315 / 3.20 ( 3018) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 0.843 Fit side-chains REVERT: A 168 GLU cc_start: 0.8434 (tm-30) cc_final: 0.7987 (tp30) REVERT: A 307 GLU cc_start: 0.7321 (tp30) cc_final: 0.7007 (tp30) REVERT: E 54 MET cc_start: 0.8517 (mmm) cc_final: 0.8297 (mmm) REVERT: F 14 ASP cc_start: 0.7099 (m-30) cc_final: 0.6706 (m-30) REVERT: G 153 SER cc_start: 0.8435 (t) cc_final: 0.8175 (m) REVERT: G 307 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6854 (pm20) REVERT: H 44 MET cc_start: 0.5996 (tpt) cc_final: 0.5096 (tpt) REVERT: H 148 TYR cc_start: 0.6127 (m-80) cc_final: 0.5653 (m-80) REVERT: H 253 LYS cc_start: 0.6094 (tptp) cc_final: 0.5817 (tptt) outliers start: 40 outliers final: 24 residues processed: 254 average time/residue: 0.1285 time to fit residues: 52.3588 Evaluate side-chains 233 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 364 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 250 optimal weight: 0.9980 chunk 203 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 132 optimal weight: 0.0970 chunk 12 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN B 35 GLN E 164 ASN G 9 ASN G 54 HIS H 37 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.190758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.156490 restraints weight = 29126.849| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.42 r_work: 0.3938 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21332 Z= 0.133 Angle : 0.547 9.484 28919 Z= 0.281 Chirality : 0.041 0.219 3346 Planarity : 0.004 0.046 3560 Dihedral : 11.424 172.284 3012 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.83 % Allowed : 13.40 % Favored : 84.77 % 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: 0.57 (0.18), residues: 2497 helix: 1.63 (0.15), residues: 1220 sheet: 0.10 (0.26), residues: 438 loop : -1.33 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 174 TYR 0.020 0.001 TYR E 92 PHE 0.018 0.001 PHE G 202 TRP 0.013 0.001 TRP E 259 HIS 0.005 0.001 HIS G 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (21332) covalent geometry : angle 0.54663 / 0.28 (28919) hydrogen bonds : bond 0.03562 / 2.42 ( 1019) hydrogen bonds : angle 4.44749 / 3.18 ( 3018) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 0.771 Fit side-chains REVERT: A 168 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7993 (tp30) REVERT: A 175 TYR cc_start: 0.7382 (m-10) cc_final: 0.6945 (m-80) REVERT: A 307 GLU cc_start: 0.7328 (tp30) cc_final: 0.7035 (tp30) REVERT: E 54 MET cc_start: 0.8497 (mmm) cc_final: 0.8292 (mmm) REVERT: F 14 ASP cc_start: 0.7112 (m-30) cc_final: 0.6724 (m-30) REVERT: G 153 SER cc_start: 0.8436 (t) cc_final: 0.8174 (m) REVERT: G 171 LYS cc_start: 0.7210 (ttpp) cc_final: 0.6973 (tptp) REVERT: G 307 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6981 (pm20) REVERT: H 148 TYR cc_start: 0.6151 (m-80) cc_final: 0.5730 (m-80) REVERT: H 253 LYS cc_start: 0.6086 (tptp) cc_final: 0.5781 (tptt) outliers start: 42 outliers final: 27 residues processed: 250 average time/residue: 0.1329 time to fit residues: 53.2928 Evaluate side-chains 238 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 247 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 157 optimal weight: 3.9990 chunk 234 optimal weight: 0.0370 chunk 111 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 211 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 GLN D 313 ASN G 9 ASN G 54 HIS H 37 ASN H 247 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.190416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.155668 restraints weight = 29071.848| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.22 r_work: 0.3947 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21332 Z= 0.124 Angle : 0.542 9.680 28919 Z= 0.277 Chirality : 0.041 0.206 3346 Planarity : 0.003 0.046 3560 Dihedral : 11.415 172.137 3012 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.74 % Allowed : 14.14 % Favored : 84.12 % 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: 0.58 (0.18), residues: 2497 helix: 1.66 (0.15), residues: 1219 sheet: 0.01 (0.26), residues: 439 loop : -1.30 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 174 TYR 0.018 0.001 TYR E 92 PHE 0.021 0.001 PHE F 246 TRP 0.020 0.001 TRP F 415 HIS 0.004 0.001 HIS G 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (21332) covalent geometry : angle 0.54245 / 0.28 (28919) hydrogen bonds : bond 0.03438 / 2.33 ( 1019) hydrogen bonds : angle 4.37514 / 3.12 ( 3018) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 216 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8024 (tp30) REVERT: A 178 MET cc_start: 0.5406 (mmm) cc_final: 0.5073 (mmt) REVERT: A 307 GLU cc_start: 0.7477 (tp30) cc_final: 0.7161 (tp30) REVERT: E 54 MET cc_start: 0.8504 (mmm) cc_final: 0.8293 (mmm) REVERT: E 255 ILE cc_start: 0.6914 (OUTLIER) cc_final: 0.6437 (mp) REVERT: F 14 ASP cc_start: 0.7178 (m-30) cc_final: 0.6767 (m-30) REVERT: F 231 MET cc_start: 0.4865 (OUTLIER) cc_final: 0.3647 (tmm) REVERT: G 153 SER cc_start: 0.8516 (t) cc_final: 0.8256 (m) REVERT: G 171 LYS cc_start: 0.7227 (ttpp) cc_final: 0.7019 (tptp) REVERT: G 307 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7118 (pt0) REVERT: H 148 TYR cc_start: 0.6115 (m-80) cc_final: 0.5696 (m-80) REVERT: H 253 LYS cc_start: 0.6094 (tptp) cc_final: 0.5796 (tptt) outliers start: 40 outliers final: 26 residues processed: 241 average time/residue: 0.1391 time to fit residues: 53.2610 Evaluate side-chains 233 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 247 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 364 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 249 optimal weight: 10.0000 chunk 140 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 206 optimal weight: 0.4980 chunk 251 optimal weight: 10.0000 chunk 197 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 GLN E 164 ASN G 9 ASN G 54 HIS H 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.189708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.154830 restraints weight = 29224.115| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.16 r_work: 0.3934 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21332 Z= 0.123 Angle : 0.538 7.404 28919 Z= 0.274 Chirality : 0.041 0.206 3346 Planarity : 0.004 0.136 3560 Dihedral : 11.407 172.062 3012 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.83 % Allowed : 14.53 % Favored : 83.64 % 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: 0.59 (0.18), residues: 2497 helix: 1.68 (0.15), residues: 1219 sheet: -0.04 (0.26), residues: 444 loop : -1.29 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG F 252 TYR 0.018 0.001 TYR E 92 PHE 0.019 0.001 PHE G 202 TRP 0.018 0.001 TRP F 415 HIS 0.005 0.001 HIS G 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (21332) covalent geometry : angle 0.53803 / 0.27 (28919) hydrogen bonds : bond 0.03404 / 2.30 ( 1019) hydrogen bonds : angle 4.33652 / 3.09 ( 3018) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8058 (tp30) REVERT: A 174 ARG cc_start: 0.7279 (mtm110) cc_final: 0.6809 (tmm-80) REVERT: A 307 GLU cc_start: 0.7517 (tp30) cc_final: 0.7167 (tp30) REVERT: B 257 TRP cc_start: 0.8148 (OUTLIER) cc_final: 0.5770 (m-90) REVERT: E 54 MET cc_start: 0.8486 (mmm) cc_final: 0.8276 (mmm) REVERT: E 142 GLU cc_start: 0.8791 (mp0) cc_final: 0.8430 (mp0) REVERT: E 255 ILE cc_start: 0.6941 (OUTLIER) cc_final: 0.6529 (mp) REVERT: F 14 ASP cc_start: 0.7244 (m-30) cc_final: 0.6843 (m-30) REVERT: G 153 SER cc_start: 0.8559 (t) cc_final: 0.8309 (m) REVERT: G 171 LYS cc_start: 0.7223 (ttpp) cc_final: 0.7008 (tptp) REVERT: G 307 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7176 (pt0) REVERT: H 148 TYR cc_start: 0.6141 (m-80) cc_final: 0.5723 (m-80) REVERT: H 253 LYS cc_start: 0.6128 (tptp) cc_final: 0.5810 (tptt) outliers start: 42 outliers final: 30 residues processed: 245 average time/residue: 0.1314 time to fit residues: 51.8845 Evaluate side-chains 234 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 137 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 27 optimal weight: 3.9990 chunk 234 optimal weight: 0.4980 chunk 165 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 245 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN D 96 ASN F 67 GLN G 9 ASN G 54 HIS H 37 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.187830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.152718 restraints weight = 29139.588| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 2.22 r_work: 0.3910 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21332 Z= 0.142 Angle : 0.558 8.900 28919 Z= 0.285 Chirality : 0.042 0.387 3346 Planarity : 0.004 0.081 3560 Dihedral : 11.440 172.295 3012 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.22 % Allowed : 14.53 % Favored : 83.25 % 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: 0.50 (0.17), residues: 2497 helix: 1.58 (0.15), residues: 1219 sheet: -0.06 (0.26), residues: 441 loop : -1.31 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 252 TYR 0.024 0.001 TYR C 71 PHE 0.025 0.001 PHE F 249 TRP 0.034 0.002 TRP F 415 HIS 0.004 0.001 HIS E 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (21332) covalent geometry : angle 0.55819 / 0.28 (28919) hydrogen bonds : bond 0.03545 / 2.38 ( 1019) hydrogen bonds : angle 4.36974 / 3.11 ( 3018) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 218 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8034 (tp30) REVERT: A 307 GLU cc_start: 0.7488 (tp30) cc_final: 0.7147 (tp30) REVERT: B 257 TRP cc_start: 0.8238 (OUTLIER) cc_final: 0.5891 (m-90) REVERT: E 142 GLU cc_start: 0.8817 (mp0) cc_final: 0.8449 (mp0) REVERT: E 255 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6613 (mp) REVERT: F 14 ASP cc_start: 0.7171 (m-30) cc_final: 0.6757 (m-30) REVERT: F 48 PRO cc_start: 0.6927 (Cg_endo) cc_final: 0.6725 (Cg_exo) REVERT: G 153 SER cc_start: 0.8578 (t) cc_final: 0.8322 (m) REVERT: G 307 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7298 (pt0) REVERT: H 148 TYR cc_start: 0.6129 (m-80) cc_final: 0.5636 (m-80) REVERT: H 253 LYS cc_start: 0.6155 (tptp) cc_final: 0.5839 (tptt) outliers start: 51 outliers final: 35 residues processed: 255 average time/residue: 0.1323 time to fit residues: 54.2423 Evaluate side-chains 245 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 364 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 167 optimal weight: 0.6980 chunk 232 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 240 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 204 optimal weight: 0.7980 chunk 211 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN G 9 ASN G 54 HIS H 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.188258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.153247 restraints weight = 29142.625| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 2.22 r_work: 0.3915 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 21332 Z= 0.126 Angle : 0.559 14.373 28919 Z= 0.282 Chirality : 0.042 0.420 3346 Planarity : 0.004 0.079 3560 Dihedral : 11.411 172.071 3012 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.87 % Allowed : 15.10 % Favored : 83.03 % 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: 0.52 (0.18), residues: 2497 helix: 1.63 (0.15), residues: 1219 sheet: -0.10 (0.26), residues: 441 loop : -1.32 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 252 TYR 0.019 0.001 TYR E 92 PHE 0.019 0.001 PHE F 249 TRP 0.034 0.002 TRP F 415 HIS 0.005 0.001 HIS G 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (21332) covalent geometry : angle 0.55907 / 0.28 (28919) hydrogen bonds : bond 0.03407 / 2.29 ( 1019) hydrogen bonds : angle 4.33166 / 3.08 ( 3018) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7971 (tp30) REVERT: A 178 MET cc_start: 0.5417 (mmm) cc_final: 0.4867 (mmt) REVERT: A 307 GLU cc_start: 0.7497 (tp30) cc_final: 0.7137 (tp30) REVERT: B 257 TRP cc_start: 0.8267 (OUTLIER) cc_final: 0.5761 (m-90) REVERT: E 142 GLU cc_start: 0.8801 (mp0) cc_final: 0.8444 (mp0) REVERT: E 255 ILE cc_start: 0.6960 (OUTLIER) cc_final: 0.6604 (mp) REVERT: F 14 ASP cc_start: 0.7247 (m-30) cc_final: 0.6870 (m-30) REVERT: F 468 ILE cc_start: 0.8705 (mm) cc_final: 0.8176 (mm) REVERT: G 153 SER cc_start: 0.8583 (t) cc_final: 0.8331 (m) REVERT: G 307 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7322 (pt0) REVERT: H 148 TYR cc_start: 0.6130 (m-80) cc_final: 0.5655 (m-80) REVERT: H 253 LYS cc_start: 0.6153 (tptp) cc_final: 0.5843 (tptt) outliers start: 43 outliers final: 35 residues processed: 245 average time/residue: 0.1457 time to fit residues: 56.9151 Evaluate side-chains 240 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 364 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 49 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 229 optimal weight: 10.0000 chunk 222 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 92 optimal weight: 0.0470 chunk 17 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN G 9 ASN G 54 HIS H 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.188402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.153574 restraints weight = 29252.218| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 2.20 r_work: 0.3921 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 21332 Z= 0.121 Angle : 0.562 14.167 28919 Z= 0.283 Chirality : 0.042 0.391 3346 Planarity : 0.004 0.066 3560 Dihedral : 11.390 171.938 3012 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.70 % Allowed : 15.32 % Favored : 82.99 % 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: 0.54 (0.18), residues: 2497 helix: 1.65 (0.15), residues: 1219 sheet: -0.12 (0.26), residues: 441 loop : -1.30 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 109 TYR 0.019 0.001 TYR E 92 PHE 0.018 0.001 PHE G 40 TRP 0.032 0.001 TRP F 415 HIS 0.005 0.001 HIS G 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (21332) covalent geometry : angle 0.56189 / 0.28 (28919) hydrogen bonds : bond 0.03344 / 2.24 ( 1019) hydrogen bonds : angle 4.30870 / 3.07 ( 3018) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7996 (tp30) REVERT: A 178 MET cc_start: 0.5285 (mmm) cc_final: 0.4915 (mmt) REVERT: A 307 GLU cc_start: 0.7505 (tp30) cc_final: 0.7154 (tp30) REVERT: B 257 TRP cc_start: 0.8263 (OUTLIER) cc_final: 0.5818 (m-90) REVERT: E 142 GLU cc_start: 0.8784 (mp0) cc_final: 0.8438 (mp0) REVERT: E 255 ILE cc_start: 0.6960 (OUTLIER) cc_final: 0.6664 (mp) REVERT: F 14 ASP cc_start: 0.7194 (m-30) cc_final: 0.6805 (m-30) REVERT: F 231 MET cc_start: 0.4880 (OUTLIER) cc_final: 0.3489 (tmm) REVERT: F 468 ILE cc_start: 0.8718 (mm) cc_final: 0.8223 (mm) REVERT: G 153 SER cc_start: 0.8586 (t) cc_final: 0.8344 (m) REVERT: G 307 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7341 (pt0) REVERT: H 148 TYR cc_start: 0.6171 (m-80) cc_final: 0.5703 (m-80) REVERT: H 253 LYS cc_start: 0.6147 (tptp) cc_final: 0.5836 (tptt) outliers start: 39 outliers final: 32 residues processed: 242 average time/residue: 0.1425 time to fit residues: 55.7493 Evaluate side-chains 242 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 246 PHE Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 54 HIS Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 364 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 60 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 98 optimal weight: 0.4980 chunk 34 optimal weight: 7.9990 chunk 19 optimal weight: 0.0670 chunk 122 optimal weight: 0.9980 chunk 138 optimal weight: 0.0770 chunk 171 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 236 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN H 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.188398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.154051 restraints weight = 29204.418| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.11 r_work: 0.3921 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.238 21332 Z= 0.277 Angle : 0.814 59.182 28919 Z= 0.515 Chirality : 0.048 1.139 3346 Planarity : 0.005 0.220 3560 Dihedral : 11.388 171.940 3012 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.65 % Allowed : 15.54 % Favored : 82.81 % Cbeta Deviations : 0.08 % 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: 0.55 (0.18), residues: 2497 helix: 1.66 (0.15), residues: 1219 sheet: -0.12 (0.26), residues: 441 loop : -1.30 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 106 TYR 0.018 0.001 TYR E 92 PHE 0.018 0.001 PHE G 40 TRP 0.029 0.001 TRP F 415 HIS 0.417 0.004 HIS G 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.28 (21332) covalent geometry : angle 0.81356 / 0.51 (28919) hydrogen bonds : bond 0.03339 / 2.24 ( 1019) hydrogen bonds : angle 4.30912 / 3.07 ( 3018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5087.73 seconds wall clock time: 88 minutes 26.28 seconds (5306.28 seconds total)