Starting phenix.real_space_refine on Tue Sep 15 21:25:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7stb_25423/09_2026/7stb_25423_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7stb_25423/09_2026/7stb_25423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7stb_25423/09_2026/7stb_25423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7stb_25423/09_2026/7stb_25423.map" model { file = "/net/cci-nas-00/data/ceres_data/7stb_25423/09_2026/7stb_25423_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7stb_25423/09_2026/7stb_25423_trim.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 49 5.49 5 Mg 4 5.21 5 S 119 5.16 5 C 14313 2.51 5 N 3904 2.21 5 O 4425 1.98 5 H 22555 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 45369 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 8378 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 19, 'TRANS': 495} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5027 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5196 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 5304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5304 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 320} Chain: "E" Number of atoms: 5525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 5525 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 4539 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 3, 'TRANS': 284} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 5428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5428 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 11, 'TRANS': 328} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4710 Classifications: {'peptide': 293} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 6 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 804 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "I" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 303 Classifications: {'DNA': 11} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 10} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 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: 7.56, per 1000 atoms: 0.17 Number of scatterers: 45369 At special positions: 0 Unit cell: (128.856, 122.248, 145.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 119 16.00 P 49 15.00 Mg 4 11.99 O 4425 8.00 N 3904 7.00 C 14313 6.00 H 22555 1.00 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: 4.37 Conformation dependent library (CDL) restraints added in 1.4 seconds 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5266 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 16 sheets defined 54.6% alpha, 17.3% beta 7 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 7.83 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.572A pdb=" N VAL A 78 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 114 through 131 removed outlier: 3.610A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 175 through 176 No H-bonds generated for 'chain 'A' and resid 175 through 176' Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 296 through 306 removed outlier: 3.757A pdb=" N VAL A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.786A pdb=" N LYS A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.990A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) 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 408 removed outlier: 3.678A pdb=" N ALA A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.603A pdb=" N ILE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 472 Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 483 through 509 Proline residue: A 489 - end of helix Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 566 through 590 Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 4.132A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.704A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.642A pdb=" N LEU B 191 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.660A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.687A pdb=" N ASN C 12 " --> pdb=" O SER C 9 " (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 44 Processing helix chain 'C' and resid 58 through 71 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 89 through 102 removed outlier: 3.967A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 137 removed outlier: 4.109A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.686A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.610A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 270 removed outlier: 4.069A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 292 through 313 removed outlier: 3.908A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 332 Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 42 through 52 removed outlier: 4.499A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 70 through 91 removed outlier: 3.602A pdb=" N THR D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) Proline residue: D 85 - end of helix removed outlier: 4.085A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.859A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.561A pdb=" N LEU D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.622A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 197 through 209 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.678A 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 292 Processing helix chain 'D' and resid 296 through 311 Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.595A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 353 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.516A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.331A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 97 through 103 removed outlier: 6.890A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.904A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 3.559A pdb=" N ARG E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR E 161 " --> pdb=" O THR E 157 " (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 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 292 removed outlier: 3.650A pdb=" N ALA E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 335 Processing helix chain 'E' and resid 338 through 354 Processing helix chain 'F' and resid 17 through 26 removed outlier: 3.606A pdb=" N ILE F 21 " --> pdb=" O HIS F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 32 Proline residue: F 30 - end of helix No H-bonds generated for 'chain 'F' and resid 27 through 32' Processing helix chain 'F' and resid 65 through 67 No H-bonds generated for 'chain 'F' and resid 65 through 67' Processing helix chain 'F' and resid 88 through 93 removed outlier: 3.570A pdb=" N VAL F 93 " --> pdb=" O ILE F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 145 removed outlier: 4.304A pdb=" N LEU F 145 " --> pdb=" O THR F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 173 Processing helix chain 'F' and resid 239 through 243 Processing helix chain 'F' and resid 245 through 251 removed outlier: 3.823A pdb=" N ILE F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 328 Processing helix chain 'G' and resid 9 through 27 Processing helix chain 'G' and resid 59 through 61 No H-bonds generated for 'chain 'G' and resid 59 through 61' Processing helix chain 'G' and resid 68 through 71 Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 98 through 106 Processing helix chain 'G' and resid 127 through 131 Processing helix chain 'G' and resid 161 through 174 Processing helix chain 'G' and resid 188 through 205 Processing helix chain 'G' and resid 234 through 244 removed outlier: 3.755A pdb=" N ASN G 243 " --> pdb=" O ASN G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 333 Processing helix chain 'G' and resid 334 through 339 Proline residue: G 337 - end of helix No H-bonds generated for 'chain 'G' and resid 334 through 339' Processing helix chain 'H' and resid 12 through 28 Processing helix chain 'H' and resid 75 through 77 No H-bonds generated for 'chain 'H' and resid 75 through 77' Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 97 through 115 removed outlier: 3.939A pdb=" N SER H 115 " --> pdb=" O MET H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 220 removed outlier: 3.711A pdb=" N ILE H 220 " --> pdb=" O GLN H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 252 Processing helix chain 'H' and resid 253 through 256 removed outlier: 3.972A pdb=" N TYR H 256 " --> pdb=" O VAL H 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 253 through 256' Processing helix chain 'H' and resid 412 through 423 Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.247A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 186 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR A 224 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 78 removed outlier: 3.540A pdb=" N LEU B 113 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N TYR B 163 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER B 48 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.145A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU C 49 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ALA C 147 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE C 51 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.997A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.172A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.695A pdb=" N ARG E 73 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.475A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 69 through 72 removed outlier: 3.660A pdb=" N SER F 127 " --> pdb=" O CYS H 295 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS H 291 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU H 281 " --> pdb=" O TRP H 296 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ASN H 286 " --> pdb=" O HIS H 261 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N HIS H 261 " --> pdb=" O ASN H 286 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS H 406 " --> pdb=" O GLY H 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 79 through 85 removed outlier: 5.948A pdb=" N ASP F 36 " --> pdb=" O GLU F 51 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU F 51 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL F 305 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS F 216 " --> pdb=" O ILE F 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 232 through 238 removed outlier: 3.634A pdb=" N GLU F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU G 63 " --> pdb=" O THR G 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 78 through 82 removed outlier: 4.304A pdb=" N SER G 93 " --> pdb=" O ILE G 155 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 78 through 82 removed outlier: 7.222A pdb=" N ASP G 29 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N MET G 44 " --> pdb=" O ASP G 29 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLN G 365 " --> pdb=" O ASN G 348 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASN G 348 " --> pdb=" O GLN G 365 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 320 through 325 removed outlier: 3.623A pdb=" N SER G 283 " --> pdb=" O LYS H 206 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS H 206 " --> pdb=" O SER G 283 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS H 122 " --> pdb=" O GLY H 157 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU H 123 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU H 3 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU H 79 " --> pdb=" O ILE H 6 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 320 through 325 removed outlier: 3.623A pdb=" N SER G 283 " --> pdb=" O LYS H 206 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS H 206 " --> pdb=" O SER G 283 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN H 96 " --> pdb=" O PRO H 208 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY H 462 " --> pdb=" O LEU H 444 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER H 443 " --> pdb=" O GLU H 427 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU H 427 " --> pdb=" O SER H 443 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 270 through 271 removed outlier: 6.363A pdb=" N VAL G 270 " --> pdb=" O LEU G 278 " (cutoff:3.500A) 1282 hydrogen bonds defined for protein. 3663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 12.15 Time building geometry restraints manager: 6.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 22500 1.06 - 1.28: 3801 1.28 - 1.50: 9706 1.50 - 1.73: 9639 1.73 - 1.95: 179 Bond restraints: 45825 Sorted by residual: bond pdb=" O3B AGS B 402 " pdb=" PB AGS B 402 " ideal model delta sigma weight residual 1.673 1.582 0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" O3B AGS A 901 " pdb=" PB AGS A 901 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" O3B AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" O3B AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sigma weight residual 1.673 1.586 0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" O3A AGS A 901 " pdb=" PA AGS A 901 " ideal model delta sigma weight residual 1.664 1.584 0.080 2.00e-02 2.50e+03 1.61e+01 ... (remaining 45820 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 82835 3.01 - 6.03: 123 6.03 - 9.04: 25 9.04 - 12.05: 6 12.05 - 15.06: 1 Bond angle restraints: 82990 Sorted by residual: angle pdb=" CA PRO E 63 " pdb=" N PRO E 63 " pdb=" CD PRO E 63 " ideal model delta sigma weight residual 112.00 96.94 15.06 1.40e+00 5.10e-01 1.16e+02 angle pdb=" N PRO E 63 " pdb=" CD PRO E 63 " pdb=" CG PRO E 63 " ideal model delta sigma weight residual 103.20 94.36 8.84 1.50e+00 4.44e-01 3.48e+01 angle pdb=" N3 DT I 7 " pdb=" C4 DT I 7 " pdb=" O4 DT I 7 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT J 23 " pdb=" C4 DT J 23 " pdb=" O4 DT J 23 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT J 29 " pdb=" C4 DT J 29 " pdb=" O4 DT J 29 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 ... (remaining 82985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.32: 20616 31.32 - 62.63: 657 62.63 - 93.95: 34 93.95 - 125.26: 1 125.26 - 156.58: 1 Dihedral angle restraints: 21309 sinusoidal: 12017 harmonic: 9292 Sorted by residual: dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 179.41 120.59 1 2.00e+01 2.50e-03 3.62e+01 dihedral pdb=" C4' DG J 12 " pdb=" C3' DG J 12 " pdb=" O3' DG J 12 " pdb=" P DA J 13 " ideal model delta sinusoidal sigma weight residual 220.00 63.42 156.58 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" CA GLU F 215 " pdb=" C GLU F 215 " pdb=" N LYS F 216 " pdb=" CA LYS F 216 " ideal model delta harmonic sigma weight residual -180.00 -162.88 -17.12 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 21306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3121 0.055 - 0.110: 381 0.110 - 0.166: 130 0.166 - 0.221: 0 0.221 - 0.276: 4 Chirality restraints: 3636 Sorted by residual: chirality pdb=" C3' AGS A 901 " pdb=" C2' AGS A 901 " pdb=" C4' AGS A 901 " pdb=" O3' AGS A 901 " both_signs ideal model delta sigma weight residual False -2.37 -2.65 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' AGS B 402 " pdb=" C2' AGS B 402 " pdb=" C4' AGS B 402 " pdb=" O3' AGS B 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C3' AGS C 402 " pdb=" C2' AGS C 402 " pdb=" C4' AGS C 402 " pdb=" O3' AGS C 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 3633 not shown) Planarity restraints: 6533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " 0.054 5.00e-02 4.00e+02 7.31e-02 8.54e+00 pdb=" N PRO E 63 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 32 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO D 33 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 33 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 33 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 162 " -0.124 9.50e-02 1.11e+02 4.15e-02 2.06e+00 pdb=" NE ARG B 162 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG B 162 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 162 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 162 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 162 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG B 162 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 162 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 162 " -0.000 2.00e-02 2.50e+03 ... (remaining 6530 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 2204 2.19 - 2.80: 93519 2.80 - 3.40: 124855 3.40 - 4.00: 167163 4.00 - 4.60: 259721 Nonbonded interactions: 647462 Sorted by model distance: nonbonded pdb=" O PHE A 387 " pdb=" HD1 HIS A 438 " model vdw 1.593 2.450 nonbonded pdb=" OD1 ASP A 402 " pdb="HH12 ARG E 331 " model vdw 1.594 2.450 nonbonded pdb=" O ARG H 20 " pdb="HD21 ASN H 24 " model vdw 1.595 2.450 nonbonded pdb=" HG1 THR A 224 " pdb=" O3G AGS A 901 " model vdw 1.596 2.450 nonbonded pdb=" H LYS D 34 " pdb=" OE2 GLU D 38 " model vdw 1.598 2.450 ... (remaining 647457 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: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.280 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 50.630 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.003 0.158 23270 Z= 0.197 Angle : 0.551 15.063 31605 Z= 0.313 Chirality : 0.042 0.276 3636 Planarity : 0.003 0.073 3878 Dihedral : 14.310 156.576 8938 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.62 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.17), residues: 2707 helix: 2.46 (0.15), residues: 1297 sheet: 0.99 (0.22), residues: 562 loop : 0.25 (0.24), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 162 TYR 0.008 0.001 TYR E 287 PHE 0.015 0.001 PHE F 236 TRP 0.006 0.001 TRP G 42 HIS 0.006 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.20 (23270) covalent geometry : angle 0.55103 / 0.31 (31605) hydrogen bonds : bond 0.13949 / 9.38 ( 1271) hydrogen bonds : angle 5.45335 / 4.01 ( 3693) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 410 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 410 average time/residue: 1.4728 time to fit residues: 691.9664 Evaluate side-chains 184 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 143 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN B 146 GLN B 208 ASN B 250 GLN C 30 GLN C 291 GLN E 19 ASN E 118 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN G 151 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.104694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.082307 restraints weight = 144348.618| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.98 r_work: 0.3392 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23270 Z= 0.193 Angle : 0.577 6.558 31605 Z= 0.313 Chirality : 0.041 0.197 3636 Planarity : 0.004 0.078 3878 Dihedral : 12.429 155.961 3478 Min Nonbonded Distance : 1.663 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 1.29 % Allowed : 9.45 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.17), residues: 2707 helix: 2.02 (0.15), residues: 1313 sheet: 0.83 (0.22), residues: 568 loop : 0.01 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 69 TYR 0.028 0.001 TYR H 422 PHE 0.017 0.001 PHE G 152 TRP 0.006 0.001 TRP G 42 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (23270) covalent geometry : angle 0.57678 / 0.31 (31605) hydrogen bonds : bond 0.04972 / 3.31 ( 1271) hydrogen bonds : angle 4.68468 / 3.44 ( 3693) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8228 (tp30) cc_final: 0.7809 (tp30) REVERT: A 146 HIS cc_start: 0.7086 (OUTLIER) cc_final: 0.6858 (t70) REVERT: B 77 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8152 (tp30) REVERT: B 218 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7594 (tm) REVERT: D 24 GLN cc_start: 0.6366 (tt0) cc_final: 0.5918 (mm-40) REVERT: D 196 ASN cc_start: 0.7564 (t0) cc_final: 0.7209 (t0) REVERT: E 118 GLN cc_start: 0.8404 (mt0) cc_final: 0.7984 (tm-30) REVERT: F 238 ASP cc_start: 0.7334 (t0) cc_final: 0.7115 (t0) REVERT: G 193 ASP cc_start: 0.7993 (m-30) cc_final: 0.7751 (m-30) REVERT: G 198 THR cc_start: 0.8084 (m) cc_final: 0.7701 (t) outliers start: 32 outliers final: 8 residues processed: 210 average time/residue: 1.4396 time to fit residues: 348.8507 Evaluate side-chains 172 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 25 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN A 89 GLN F 17 HIS ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN G 69 HIS G 247 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.102753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.079799 restraints weight = 143930.744| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.07 r_work: 0.3339 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23270 Z= 0.163 Angle : 0.523 7.432 31605 Z= 0.283 Chirality : 0.040 0.203 3636 Planarity : 0.004 0.054 3878 Dihedral : 12.080 155.330 3476 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 0.97 % Allowed : 10.74 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.17), residues: 2707 helix: 1.96 (0.15), residues: 1310 sheet: 0.69 (0.22), residues: 567 loop : -0.15 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 149 TYR 0.010 0.001 TYR G 229 PHE 0.017 0.001 PHE G 152 TRP 0.012 0.001 TRP A 294 HIS 0.006 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (23270) covalent geometry : angle 0.52321 / 0.28 (31605) hydrogen bonds : bond 0.04390 / 2.95 ( 1271) hydrogen bonds : angle 4.49442 / 3.30 ( 3693) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8398 (tp30) cc_final: 0.7945 (tp30) REVERT: A 238 PHE cc_start: 0.5637 (OUTLIER) cc_final: 0.5244 (m-80) REVERT: A 584 TYR cc_start: 0.6399 (OUTLIER) cc_final: 0.6186 (t80) REVERT: B 279 GLN cc_start: 0.7908 (mp10) cc_final: 0.7669 (mp10) REVERT: D 24 GLN cc_start: 0.6408 (tt0) cc_final: 0.5930 (mm-40) REVERT: D 81 GLU cc_start: 0.7961 (mp0) cc_final: 0.7720 (mp0) REVERT: E 76 VAL cc_start: 0.8677 (t) cc_final: 0.8468 (m) REVERT: E 118 GLN cc_start: 0.8314 (mt0) cc_final: 0.7893 (tm-30) REVERT: F 238 ASP cc_start: 0.7328 (t0) cc_final: 0.7098 (t0) REVERT: G 193 ASP cc_start: 0.8051 (m-30) cc_final: 0.7746 (m-30) outliers start: 24 outliers final: 10 residues processed: 188 average time/residue: 1.3348 time to fit residues: 294.0945 Evaluate side-chains 169 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 42 optimal weight: 4.9990 chunk 208 optimal weight: 8.9990 chunk 197 optimal weight: 0.8980 chunk 229 optimal weight: 4.9990 chunk 263 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.102103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.079186 restraints weight = 144242.917| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.03 r_work: 0.3330 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23270 Z= 0.149 Angle : 0.517 6.785 31605 Z= 0.280 Chirality : 0.040 0.208 3636 Planarity : 0.004 0.046 3878 Dihedral : 12.103 155.642 3474 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 1.01 % Allowed : 11.23 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.17), residues: 2707 helix: 1.95 (0.15), residues: 1317 sheet: 0.61 (0.22), residues: 567 loop : -0.21 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 149 TYR 0.060 0.001 TYR C 288 PHE 0.016 0.001 PHE G 152 TRP 0.007 0.001 TRP G 42 HIS 0.006 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (23270) covalent geometry : angle 0.51701 / 0.28 (31605) hydrogen bonds : bond 0.03937 / 2.65 ( 1271) hydrogen bonds : angle 4.36997 / 3.21 ( 3693) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8420 (tp30) cc_final: 0.7943 (tp30) REVERT: A 238 PHE cc_start: 0.5635 (OUTLIER) cc_final: 0.5240 (m-80) REVERT: C 167 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8502 (pt0) REVERT: D 24 GLN cc_start: 0.6519 (tt0) cc_final: 0.6037 (mm-40) REVERT: D 81 GLU cc_start: 0.7983 (mp0) cc_final: 0.7717 (mp0) REVERT: E 118 GLN cc_start: 0.8285 (mt0) cc_final: 0.7888 (tm-30) REVERT: F 238 ASP cc_start: 0.7314 (t0) cc_final: 0.7069 (t0) REVERT: G 167 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8004 (mppt) REVERT: G 193 ASP cc_start: 0.8132 (m-30) cc_final: 0.7808 (m-30) outliers start: 25 outliers final: 8 residues processed: 186 average time/residue: 1.3410 time to fit residues: 292.1268 Evaluate side-chains 170 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain E residue 272 LYS Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 167 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 147 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 193 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 247 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN G 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.101210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.078264 restraints weight = 144162.889| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.04 r_work: 0.3313 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23270 Z= 0.170 Angle : 0.517 7.104 31605 Z= 0.278 Chirality : 0.040 0.204 3636 Planarity : 0.004 0.047 3878 Dihedral : 12.198 155.740 3474 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Rotamer: Outliers : 1.17 % Allowed : 11.63 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.17), residues: 2707 helix: 1.93 (0.15), residues: 1319 sheet: 0.57 (0.22), residues: 561 loop : -0.23 (0.23), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 149 TYR 0.046 0.001 TYR C 288 PHE 0.017 0.001 PHE G 152 TRP 0.008 0.001 TRP G 42 HIS 0.006 0.001 HIS H 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (23270) covalent geometry : angle 0.51667 / 0.28 (31605) hydrogen bonds : bond 0.04035 / 2.73 ( 1271) hydrogen bonds : angle 4.36101 / 3.20 ( 3693) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8480 (tp30) cc_final: 0.7957 (tp30) REVERT: A 238 PHE cc_start: 0.5647 (OUTLIER) cc_final: 0.5265 (m-80) REVERT: D 24 GLN cc_start: 0.6602 (tt0) cc_final: 0.6103 (mm-40) REVERT: D 81 GLU cc_start: 0.8074 (mp0) cc_final: 0.7866 (mp0) REVERT: E 118 GLN cc_start: 0.8307 (mt0) cc_final: 0.7900 (tm-30) REVERT: F 20 HIS cc_start: 0.6780 (m-70) cc_final: 0.6333 (m90) REVERT: F 238 ASP cc_start: 0.7304 (t0) cc_final: 0.7051 (t0) REVERT: G 167 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8002 (mppt) REVERT: G 193 ASP cc_start: 0.8138 (m-30) cc_final: 0.7795 (m-30) outliers start: 29 outliers final: 12 residues processed: 182 average time/residue: 1.3547 time to fit residues: 288.3034 Evaluate side-chains 165 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 284 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN H 8 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.099290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.076380 restraints weight = 144971.512| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.00 r_work: 0.3257 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23270 Z= 0.228 Angle : 0.547 7.466 31605 Z= 0.295 Chirality : 0.041 0.206 3636 Planarity : 0.004 0.052 3878 Dihedral : 12.338 155.389 3474 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 1.29 % Allowed : 11.91 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.17), residues: 2707 helix: 1.76 (0.14), residues: 1323 sheet: 0.48 (0.22), residues: 568 loop : -0.34 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 165 TYR 0.013 0.001 TYR A 501 PHE 0.023 0.002 PHE G 152 TRP 0.011 0.001 TRP G 16 HIS 0.007 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.23 (23270) covalent geometry : angle 0.54651 / 0.30 (31605) hydrogen bonds : bond 0.04373 / 2.97 ( 1271) hydrogen bonds : angle 4.44535 / 3.25 ( 3693) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8540 (tp30) cc_final: 0.8002 (tp30) REVERT: A 238 PHE cc_start: 0.5708 (OUTLIER) cc_final: 0.5311 (m-80) REVERT: D 24 GLN cc_start: 0.6872 (tt0) cc_final: 0.6312 (mm-40) REVERT: E 118 GLN cc_start: 0.8318 (mt0) cc_final: 0.7919 (tm-30) REVERT: F 20 HIS cc_start: 0.6809 (m-70) cc_final: 0.6350 (m90) REVERT: G 167 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7978 (mppt) REVERT: G 193 ASP cc_start: 0.8124 (m-30) cc_final: 0.7745 (m-30) outliers start: 32 outliers final: 15 residues processed: 172 average time/residue: 1.3060 time to fit residues: 263.0484 Evaluate side-chains 168 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 272 LYS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 198 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 0.9990 chunk 266 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 205 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 240 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.099949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.077142 restraints weight = 144037.329| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.98 r_work: 0.3279 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23270 Z= 0.151 Angle : 0.516 7.695 31605 Z= 0.277 Chirality : 0.040 0.205 3636 Planarity : 0.004 0.050 3878 Dihedral : 12.326 155.236 3474 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 1.05 % Allowed : 12.68 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.17), residues: 2707 helix: 1.81 (0.15), residues: 1326 sheet: 0.48 (0.22), residues: 567 loop : -0.29 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 149 TYR 0.011 0.001 TYR G 148 PHE 0.016 0.001 PHE G 152 TRP 0.009 0.001 TRP G 42 HIS 0.006 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (23270) covalent geometry : angle 0.51647 / 0.28 (31605) hydrogen bonds : bond 0.03996 / 2.71 ( 1271) hydrogen bonds : angle 4.36267 / 3.20 ( 3693) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8537 (tp30) cc_final: 0.7992 (tp30) REVERT: A 238 PHE cc_start: 0.5702 (OUTLIER) cc_final: 0.5304 (m-80) REVERT: D 24 GLN cc_start: 0.6846 (tt0) cc_final: 0.6322 (mm-40) REVERT: D 88 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8089 (mtm) REVERT: E 118 GLN cc_start: 0.8303 (mt0) cc_final: 0.7921 (tm-30) REVERT: F 20 HIS cc_start: 0.6772 (m-70) cc_final: 0.6327 (m90) REVERT: G 167 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8034 (mppt) REVERT: G 193 ASP cc_start: 0.8142 (m-30) cc_final: 0.7749 (m-30) outliers start: 26 outliers final: 15 residues processed: 175 average time/residue: 1.1492 time to fit residues: 235.5101 Evaluate side-chains 170 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain E residue 272 LYS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 72 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 232 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.099590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.076771 restraints weight = 144904.553| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.99 r_work: 0.3269 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23270 Z= 0.171 Angle : 0.523 7.769 31605 Z= 0.281 Chirality : 0.040 0.205 3636 Planarity : 0.004 0.052 3878 Dihedral : 12.358 155.151 3474 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 1.01 % Allowed : 13.05 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.17), residues: 2707 helix: 1.80 (0.15), residues: 1326 sheet: 0.45 (0.22), residues: 567 loop : -0.30 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 149 TYR 0.011 0.001 TYR G 148 PHE 0.017 0.001 PHE G 152 TRP 0.009 0.001 TRP G 42 HIS 0.005 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (23270) covalent geometry : angle 0.52298 / 0.28 (31605) hydrogen bonds : bond 0.04020 / 2.74 ( 1271) hydrogen bonds : angle 4.34431 / 3.19 ( 3693) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8549 (tp30) cc_final: 0.7997 (tp30) REVERT: A 238 PHE cc_start: 0.5752 (OUTLIER) cc_final: 0.5367 (m-80) REVERT: D 24 GLN cc_start: 0.6893 (tt0) cc_final: 0.6359 (mm-40) REVERT: E 118 GLN cc_start: 0.8302 (mt0) cc_final: 0.7921 (tm-30) REVERT: F 20 HIS cc_start: 0.6773 (m-70) cc_final: 0.6328 (m90) REVERT: G 167 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8020 (mppt) REVERT: G 193 ASP cc_start: 0.8125 (m-30) cc_final: 0.7739 (m-30) outliers start: 25 outliers final: 16 residues processed: 169 average time/residue: 1.1789 time to fit residues: 232.0415 Evaluate side-chains 170 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain E residue 272 LYS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 179 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 chunk 266 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.099450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.076716 restraints weight = 144289.631| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.99 r_work: 0.3270 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23270 Z= 0.164 Angle : 0.522 7.945 31605 Z= 0.280 Chirality : 0.040 0.205 3636 Planarity : 0.004 0.053 3878 Dihedral : 12.373 155.094 3474 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 1.01 % Allowed : 13.25 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.17), residues: 2707 helix: 1.80 (0.15), residues: 1327 sheet: 0.43 (0.22), residues: 567 loop : -0.32 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 149 TYR 0.011 0.001 TYR G 148 PHE 0.017 0.001 PHE C 166 TRP 0.009 0.001 TRP G 42 HIS 0.005 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (23270) covalent geometry : angle 0.52184 / 0.28 (31605) hydrogen bonds : bond 0.03977 / 2.71 ( 1271) hydrogen bonds : angle 4.32647 / 3.17 ( 3693) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8551 (tp30) cc_final: 0.7990 (tp30) REVERT: A 238 PHE cc_start: 0.5723 (OUTLIER) cc_final: 0.5333 (m-80) REVERT: C 167 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8280 (pm20) REVERT: D 24 GLN cc_start: 0.6910 (tt0) cc_final: 0.6391 (mm-40) REVERT: E 118 GLN cc_start: 0.8322 (mt0) cc_final: 0.7947 (tm-30) REVERT: F 20 HIS cc_start: 0.6765 (m-70) cc_final: 0.6315 (m90) REVERT: G 167 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8044 (mppt) REVERT: G 193 ASP cc_start: 0.8149 (m-30) cc_final: 0.7758 (m-30) REVERT: H 231 MET cc_start: 0.6773 (OUTLIER) cc_final: 0.6571 (pmt) outliers start: 25 outliers final: 17 residues processed: 170 average time/residue: 1.1642 time to fit residues: 229.6837 Evaluate side-chains 174 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 272 LYS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 197 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 165 optimal weight: 0.0470 chunk 113 optimal weight: 2.9990 chunk 272 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.099113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.076349 restraints weight = 145339.419| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.99 r_work: 0.3261 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23270 Z= 0.185 Angle : 0.537 10.411 31605 Z= 0.288 Chirality : 0.040 0.204 3636 Planarity : 0.004 0.055 3878 Dihedral : 12.405 155.082 3474 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 0.85 % Allowed : 13.45 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.17), residues: 2707 helix: 1.77 (0.15), residues: 1325 sheet: 0.39 (0.21), residues: 567 loop : -0.35 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 149 TYR 0.013 0.001 TYR A 501 PHE 0.018 0.001 PHE G 152 TRP 0.009 0.001 TRP G 16 HIS 0.005 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (23270) covalent geometry : angle 0.53663 / 0.29 (31605) hydrogen bonds : bond 0.04065 / 2.77 ( 1271) hydrogen bonds : angle 4.34881 / 3.19 ( 3693) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8566 (tp30) cc_final: 0.8007 (tp30) REVERT: A 238 PHE cc_start: 0.5745 (OUTLIER) cc_final: 0.5362 (m-80) REVERT: D 24 GLN cc_start: 0.6947 (tt0) cc_final: 0.6408 (mm-40) REVERT: E 118 GLN cc_start: 0.8335 (mt0) cc_final: 0.7949 (tm-30) REVERT: F 20 HIS cc_start: 0.6783 (m-70) cc_final: 0.6318 (m90) REVERT: G 167 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8048 (mppt) REVERT: G 193 ASP cc_start: 0.8136 (m-30) cc_final: 0.7752 (m-30) outliers start: 21 outliers final: 17 residues processed: 165 average time/residue: 1.0336 time to fit residues: 198.6858 Evaluate side-chains 169 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 272 LYS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 231 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 272 optimal weight: 9.9990 chunk 237 optimal weight: 0.9990 chunk 208 optimal weight: 0.4980 chunk 121 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 265 optimal weight: 10.0000 chunk 195 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.100821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.078583 restraints weight = 144787.384| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.88 r_work: 0.3290 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23270 Z= 0.121 Angle : 0.510 8.047 31605 Z= 0.272 Chirality : 0.040 0.204 3636 Planarity : 0.004 0.054 3878 Dihedral : 12.367 155.111 3474 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.56 % Rotamer: Outliers : 0.85 % Allowed : 13.53 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.17), residues: 2707 helix: 1.88 (0.15), residues: 1326 sheet: 0.43 (0.22), residues: 567 loop : -0.26 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 149 TYR 0.014 0.001 TYR B 186 PHE 0.019 0.001 PHE A 523 TRP 0.010 0.001 TRP G 42 HIS 0.004 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (23270) covalent geometry : angle 0.50980 / 0.27 (31605) hydrogen bonds : bond 0.03709 / 2.53 ( 1271) hydrogen bonds : angle 4.25469 / 3.13 ( 3693) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11159.44 seconds wall clock time: 189 minutes 44.55 seconds (11384.55 seconds total)