Starting phenix.real_space_refine on Sun Sep 13 05:43:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sgz_25121/09_2026/7sgz_25121.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sgz_25121/09_2026/7sgz_25121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sgz_25121/09_2026/7sgz_25121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sgz_25121/09_2026/7sgz_25121.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sgz_25121/09_2026/7sgz_25121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sgz_25121/09_2026/7sgz_25121.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7sgz_25121/09_2026/7sgz_25121.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sgz_25121/09_2026/7sgz_25121.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 37 5.49 5 Mg 4 5.21 5 S 115 5.16 5 C 13246 2.51 5 N 3615 2.21 5 O 4038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 21055 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3416 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 401} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2489 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "C" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2569 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2617 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2693 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "F" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2178 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 8, 'TRANS': 260} Chain breaks: 6 Chain: "G" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2313 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 4, 'TRANS': 287} Chain breaks: 1 Chain: "H" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2154 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 4 Chain: "P" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.98, per 1000 atoms: 0.19 Number of scatterers: 21055 At special positions: 0 Unit cell: (124.2, 125.028, 140.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 115 16.00 P 37 15.00 Mg 4 11.99 O 4038 8.00 N 3615 7.00 C 13246 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 708.9 milliseconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4898 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 16 sheets defined 52.2% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 81 through 96 removed outlier: 3.736A pdb=" N ALA A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 161 through 175 removed outlier: 3.759A pdb=" N PHE A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 removed outlier: 3.703A pdb=" N PHE A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLN A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE A 205 " --> pdb=" O PHE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.536A pdb=" N MET A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 284 through 291 removed outlier: 4.032A pdb=" N LYS A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 367 removed outlier: 3.621A pdb=" N MET A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.693A pdb=" N LEU A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 384 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 393 through 408 Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 413 through 431 Processing helix chain 'A' and resid 432 through 435 removed outlier: 3.531A pdb=" N GLY A 435 " --> pdb=" O SER A 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 432 through 435' Processing helix chain 'A' and resid 445 through 468 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.842A pdb=" N ASN A 479 " --> pdb=" O HIS A 475 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.512A pdb=" N CYS A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 68 through 75 removed outlier: 4.079A pdb=" N VAL B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 98 removed outlier: 3.658A pdb=" N GLN B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 135 Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.878A pdb=" N LYS B 149 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.726A pdb=" N GLN B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 151 through 157' Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 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 257 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 302 Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.960A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) 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 72 Processing helix chain 'C' and resid 89 through 101 removed outlier: 4.218A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.839A pdb=" N ALA C 121 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.683A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.509A pdb=" N LEU C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 4.151A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.553A pdb=" N VAL C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 217 " --> pdb=" O GLN C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 256 through 271 removed outlier: 4.046A 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 293 through 313 Processing helix chain 'C' and resid 315 through 331 Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 39 removed outlier: 3.727A pdb=" N VAL D 39 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 54 removed outlier: 3.568A pdb=" N VAL D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 84 through 91 removed outlier: 4.467A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 114 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 160 removed outlier: 4.393A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 193 through 209 removed outlier: 5.177A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 228 through 246 Processing helix chain 'D' and resid 252 through 260 removed outlier: 3.554A 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 removed outlier: 3.520A pdb=" N ILE D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 311 removed outlier: 3.620A pdb=" N VAL D 300 " --> pdb=" O SER D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.150A pdb=" N THR E 23 " --> pdb=" O ASN E 19 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 105 through 118 removed outlier: 3.514A pdb=" N ILE E 109 " --> pdb=" O ASP E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 removed outlier: 3.675A pdb=" N LEU E 146 " --> pdb=" O ALA E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 143 through 146' Processing helix chain 'E' and resid 148 through 161 Processing helix chain 'E' and resid 178 through 185 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 226 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 291 Processing helix chain 'E' and resid 295 through 308 removed outlier: 4.141A pdb=" N ILE E 299 " --> pdb=" O PRO E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 335 removed outlier: 3.635A pdb=" N LEU E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 354 Processing helix chain 'F' and resid 12 through 19 removed outlier: 4.193A pdb=" N TYR F 16 " --> pdb=" O ALA F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 30 removed outlier: 4.378A pdb=" N ILE F 23 " --> pdb=" O LEU F 19 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL F 26 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 109 removed outlier: 3.761A pdb=" N LEU F 101 " --> pdb=" O CYS F 97 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL F 103 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 221 removed outlier: 3.679A pdb=" N ILE F 220 " --> pdb=" O GLN F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 257 removed outlier: 3.525A pdb=" N SER F 244 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU F 254 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 removed outlier: 4.389A pdb=" N CYS F 418 " --> pdb=" O ASP F 414 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS F 420 " --> pdb=" O LYS F 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 26 removed outlier: 4.245A pdb=" N ILE G 21 " --> pdb=" O HIS G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 29 No H-bonds generated for 'chain 'G' and resid 27 through 29' Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 85 through 95 removed outlier: 3.884A pdb=" N ILE G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL G 93 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER G 94 " --> pdb=" O LEU G 90 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 150 No H-bonds generated for 'chain 'G' and resid 148 through 150' Processing helix chain 'G' and resid 160 through 174 removed outlier: 3.607A pdb=" N GLU G 172 " --> pdb=" O LYS G 168 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY G 174 " --> pdb=" O LEU G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 249 removed outlier: 3.619A pdb=" N LYS G 244 " --> pdb=" O THR G 240 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS G 247 " --> pdb=" O ASP G 243 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 330 removed outlier: 3.982A pdb=" N GLU G 323 " --> pdb=" O ALA G 319 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU G 325 " --> pdb=" O GLN G 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 27 removed outlier: 3.588A pdb=" N TRP H 16 " --> pdb=" O LYS H 12 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE H 26 " --> pdb=" O VAL H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 61 Processing helix chain 'H' and resid 98 through 103 removed outlier: 3.526A pdb=" N THR H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 209 Processing helix chain 'H' and resid 233 through 242 removed outlier: 3.623A pdb=" N LEU H 237 " --> pdb=" O ASN H 233 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN H 239 " --> pdb=" O THR H 235 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE H 240 " --> pdb=" O LEU H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 244 No H-bonds generated for 'chain 'H' and resid 243 through 244' Processing helix chain 'H' and resid 245 through 249 removed outlier: 3.660A pdb=" N VAL H 248 " --> pdb=" O ASN H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 339 removed outlier: 3.552A pdb=" N PHE H 332 " --> pdb=" O ASP H 328 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE H 333 " --> pdb=" O PHE H 329 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR H 334 " --> pdb=" O LYS H 330 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE H 335 " --> pdb=" O ASN H 331 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLY H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) Proline residue: H 337 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.187A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 186 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N THR A 224 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 261 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 108 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 109 through 114 removed outlier: 5.923A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 82 removed outlier: 3.693A pdb=" N ILE C 114 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 49 " --> pdb=" O PHE C 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.708A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.332A pdb=" N LEU D 93 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR D 64 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 93 through 96 removed outlier: 4.366A pdb=" N ASN E 141 " --> pdb=" O ILE E 96 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 73 through 76 removed outlier: 3.691A pdb=" N ARG E 73 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 4 through 6 removed outlier: 7.081A pdb=" N LYS F 4 " --> pdb=" O TYR F 80 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR F 80 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG F 78 " --> pdb=" O ILE F 6 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 70 through 71 removed outlier: 3.863A pdb=" N CYS F 70 " --> pdb=" O ILE F 45 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE F 45 " --> pdb=" O CYS F 70 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 42 " --> pdb=" O ASN F 38 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA F 33 " --> pdb=" O CYS F 95 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS F 95 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 120 through 124 removed outlier: 3.949A pdb=" N THR F 120 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY F 157 " --> pdb=" O LYS F 122 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR H 264 " --> pdb=" O LYS H 253 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE H 322 " --> pdb=" O LEU H 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 231 through 233 removed outlier: 3.688A pdb=" N HIS F 434 " --> pdb=" O CYS F 438 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS F 438 " --> pdb=" O HIS F 434 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 231 through 233 removed outlier: 3.688A pdb=" N HIS F 434 " --> pdb=" O CYS F 438 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS F 438 " --> pdb=" O HIS F 434 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL F 439 " --> pdb=" O ILE F 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 409 through 411 removed outlier: 3.910A pdb=" N ILE F 409 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU F 264 " --> pdb=" O ILE F 409 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS F 282 " --> pdb=" O MET F 265 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS F 291 " --> pdb=" O GLU G 131 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU F 293 " --> pdb=" O ARG G 129 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA G 13 " --> pdb=" O LEU G 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 80 through 84 removed outlier: 4.166A pdb=" N MET G 80 " --> pdb=" O ILE G 41 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE G 41 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU G 82 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL G 49 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 232 through 238 removed outlier: 4.051A pdb=" N GLU G 177 " --> pdb=" O LYS G 197 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE G 205 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE G 202 " --> pdb=" O CYS H 149 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR H 117 " --> pdb=" O VAL H 137 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 92 through 97 removed outlier: 6.908A pdb=" N ASP H 29 " --> pdb=" O MET H 44 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N MET H 44 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP H 42 " --> pdb=" O LYS H 31 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER H 43 " --> pdb=" O CYS H 52 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N CYS H 52 " --> pdb=" O SER H 43 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU H 371 " --> pdb=" O MET H 364 " (cutoff:3.500A) 1023 hydrogen bonds defined for protein. 2952 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6902 1.36 - 1.51: 5541 1.51 - 1.66: 8844 1.66 - 1.80: 85 1.80 - 1.95: 87 Bond restraints: 21459 Sorted by residual: bond pdb=" C3' DA T 22 " pdb=" C2' DA T 22 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" O3 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.79e+00 bond pdb=" O4 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.52e+00 bond pdb=" O2 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.567 1.511 0.056 2.00e-02 2.50e+03 7.96e+00 bond pdb=" O1 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.565 1.510 0.055 2.00e-02 2.50e+03 7.56e+00 ... (remaining 21454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 28332 1.44 - 2.88: 607 2.88 - 4.33: 107 4.33 - 5.77: 41 5.77 - 7.21: 12 Bond angle restraints: 29099 Sorted by residual: angle pdb=" N3 DT T 28 " pdb=" C4 DT T 28 " pdb=" O4 DT T 28 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT P 9 " pdb=" C4 DT P 9 " pdb=" O4 DT P 9 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT T 32 " pdb=" C4 DT T 32 " pdb=" O4 DT T 32 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT T 33 " pdb=" C4 DT T 33 " pdb=" O4 DT T 33 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT T 31 " pdb=" C4 DT T 31 " pdb=" O4 DT T 31 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 ... (remaining 29094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 12689 35.06 - 70.12: 325 70.12 - 105.19: 20 105.19 - 140.25: 1 140.25 - 175.31: 1 Dihedral angle restraints: 13036 sinusoidal: 5526 harmonic: 7510 Sorted by residual: dihedral pdb=" O1B ADP E 402 " pdb=" O3A ADP E 402 " pdb=" PB ADP E 402 " pdb=" PA ADP E 402 " ideal model delta sinusoidal sigma weight residual 300.00 179.88 120.12 1 2.00e+01 2.50e-03 3.60e+01 dihedral pdb=" C4' DA T 22 " pdb=" C3' DA T 22 " pdb=" O3' DA T 22 " pdb=" P DG T 23 " ideal model delta sinusoidal sigma weight residual -140.00 35.31 -175.31 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ASP A 87 " pdb=" C ASP A 87 " pdb=" N VAL A 88 " pdb=" CA VAL A 88 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 13033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3076 0.071 - 0.142: 281 0.142 - 0.212: 6 0.212 - 0.283: 0 0.283 - 0.354: 1 Chirality restraints: 3364 Sorted by residual: chirality pdb=" CB ILE G 251 " pdb=" CA ILE G 251 " pdb=" CG1 ILE G 251 " pdb=" CG2 ILE G 251 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CB VAL F 110 " pdb=" CA VAL F 110 " pdb=" CG1 VAL F 110 " pdb=" CG2 VAL F 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR G 29 " pdb=" N THR G 29 " pdb=" C THR G 29 " pdb=" CB THR G 29 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 3361 not shown) Planarity restraints: 3585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 298 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO F 299 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO F 299 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 299 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 143 " -0.009 2.00e-02 2.50e+03 1.60e-02 4.49e+00 pdb=" CG PHE C 143 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE C 143 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE C 143 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE C 143 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 143 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 143 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 42 " -0.012 2.00e-02 2.50e+03 1.23e-02 3.81e+00 pdb=" CG TRP H 42 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP H 42 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP H 42 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 42 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 42 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 42 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 42 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 42 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 42 " -0.001 2.00e-02 2.50e+03 ... (remaining 3582 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 358 2.68 - 3.24: 19758 3.24 - 3.79: 32659 3.79 - 4.35: 43072 4.35 - 4.90: 71532 Nonbonded interactions: 167379 Sorted by model distance: nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.128 2.170 nonbonded pdb=" OG1 THR D 72 " pdb="MG MG E 401 " model vdw 2.136 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.141 2.170 nonbonded pdb=" O3A AGS A 701 " pdb="MG MG A 702 " model vdw 2.144 2.170 nonbonded pdb=" O2B AGS D 500 " pdb=" O3G AGS D 500 " model vdw 2.202 3.040 ... (remaining 167374 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: 6.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.440 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.780 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 21459 Z= 0.150 Angle : 0.545 7.209 29099 Z= 0.302 Chirality : 0.041 0.354 3364 Planarity : 0.003 0.055 3585 Dihedral : 15.176 175.309 8138 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.04 % Allowed : 0.48 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.17), residues: 2516 helix: 0.92 (0.15), residues: 1167 sheet: 0.43 (0.27), residues: 453 loop : -1.22 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 157 TYR 0.013 0.001 TYR F 422 PHE 0.035 0.001 PHE C 143 TRP 0.033 0.001 TRP H 42 HIS 0.009 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.15 (21459) covalent geometry : angle 0.54505 / 0.30 (29099) hydrogen bonds : bond 0.20148 / 13.45 ( 1017) hydrogen bonds : angle 7.25374 / 5.14 ( 2952) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 318 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: E 1 MET cc_start: 0.4026 (ppp) cc_final: 0.3670 (ptm) REVERT: F 241 GLU cc_start: 0.7240 (mp0) cc_final: 0.5624 (mp0) REVERT: F 242 PHE cc_start: 0.7400 (t80) cc_final: 0.7184 (t80) REVERT: G 36 ASP cc_start: 0.7259 (m-30) cc_final: 0.7039 (m-30) REVERT: G 64 ARG cc_start: 0.7544 (tmm-80) cc_final: 0.6512 (tpt90) REVERT: G 170 LEU cc_start: 0.7220 (tp) cc_final: 0.6974 (tp) outliers start: 1 outliers final: 0 residues processed: 319 average time/residue: 0.1465 time to fit residues: 72.0100 Evaluate side-chains 247 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 0.0870 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 341 HIS B 64 HIS C 77 ASN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN D 209 ASN D 305 HIS ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 GLN G 52 ASN G 88 HIS H 97 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.182933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.144104 restraints weight = 27997.924| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.60 r_work: 0.3676 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 21459 Z= 0.238 Angle : 0.655 9.178 29099 Z= 0.342 Chirality : 0.046 0.201 3364 Planarity : 0.005 0.100 3585 Dihedral : 11.742 173.173 3032 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.34 % Allowed : 9.34 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.17), residues: 2516 helix: 0.94 (0.15), residues: 1178 sheet: 0.46 (0.26), residues: 466 loop : -1.32 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 177 TYR 0.028 0.002 TYR F 16 PHE 0.024 0.002 PHE G 48 TRP 0.017 0.002 TRP H 42 HIS 0.007 0.001 HIS C 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (21459) covalent geometry : angle 0.65509 / 0.34 (29099) hydrogen bonds : bond 0.05195 / 3.42 ( 1017) hydrogen bonds : angle 5.54907 / 3.87 ( 2952) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 264 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 403 CYS cc_start: 0.7462 (m) cc_final: 0.7162 (m) REVERT: D 115 ARG cc_start: 0.7613 (mtp85) cc_final: 0.7343 (mtm-85) REVERT: D 123 LYS cc_start: 0.8069 (pttp) cc_final: 0.7807 (tppt) REVERT: E 71 ASP cc_start: 0.7524 (p0) cc_final: 0.7264 (p0) REVERT: E 207 THR cc_start: 0.8152 (m) cc_final: 0.7835 (p) REVERT: E 273 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6995 (mt-10) REVERT: F 241 GLU cc_start: 0.7110 (mp0) cc_final: 0.5859 (mp0) REVERT: F 242 PHE cc_start: 0.7293 (t80) cc_final: 0.7060 (t80) REVERT: G 36 ASP cc_start: 0.7750 (m-30) cc_final: 0.7467 (m-30) outliers start: 31 outliers final: 20 residues processed: 282 average time/residue: 0.1536 time to fit residues: 66.3016 Evaluate side-chains 253 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 305 HIS Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 233 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 198 optimal weight: 0.6980 chunk 200 optimal weight: 0.0570 chunk 189 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 77 ASN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 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 = 0.4325 r_free = 0.4325 target = 0.184936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.145959 restraints weight = 27988.296| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.60 r_work: 0.3716 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21459 Z= 0.118 Angle : 0.534 8.516 29099 Z= 0.276 Chirality : 0.041 0.228 3364 Planarity : 0.003 0.053 3585 Dihedral : 11.675 171.830 3032 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.47 % Allowed : 11.72 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.18), residues: 2516 helix: 1.27 (0.16), residues: 1185 sheet: 0.46 (0.26), residues: 461 loop : -1.37 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 411 TYR 0.017 0.001 TYR F 256 PHE 0.018 0.001 PHE G 121 TRP 0.011 0.001 TRP H 42 HIS 0.005 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (21459) covalent geometry : angle 0.53382 / 0.28 (29099) hydrogen bonds : bond 0.04028 / 2.64 ( 1017) hydrogen bonds : angle 5.09628 / 3.56 ( 2952) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 252 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.7499 (mmtm) cc_final: 0.7296 (mmtt) REVERT: C 45 LYS cc_start: 0.6521 (ttmt) cc_final: 0.6203 (tppt) REVERT: C 50 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7946 (tp) REVERT: C 284 ILE cc_start: 0.8714 (tt) cc_final: 0.8309 (mm) REVERT: D 115 ARG cc_start: 0.7342 (mtp85) cc_final: 0.7125 (mtm-85) REVERT: D 123 LYS cc_start: 0.8059 (pttp) cc_final: 0.7799 (tppt) REVERT: D 227 ASP cc_start: 0.8370 (p0) cc_final: 0.7983 (p0) REVERT: E 71 ASP cc_start: 0.7446 (p0) cc_final: 0.7234 (p0) REVERT: E 95 GLU cc_start: 0.7572 (tp30) cc_final: 0.7305 (tp30) REVERT: E 207 THR cc_start: 0.8186 (m) cc_final: 0.7849 (p) REVERT: E 273 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6861 (mt-10) REVERT: F 241 GLU cc_start: 0.6923 (mp0) cc_final: 0.5803 (mp0) REVERT: F 242 PHE cc_start: 0.7315 (t80) cc_final: 0.7035 (t80) REVERT: G 36 ASP cc_start: 0.7676 (m-30) cc_final: 0.7422 (m-30) REVERT: G 185 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7181 (mm-30) REVERT: G 312 GLU cc_start: 0.7278 (tt0) cc_final: 0.7072 (tt0) REVERT: H 65 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6332 (pt0) outliers start: 34 outliers final: 20 residues processed: 275 average time/residue: 0.1526 time to fit residues: 64.6770 Evaluate side-chains 259 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 238 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 305 HIS Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 149 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 127 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 189 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 226 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 247 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS D 338 ASN E 144 ASN ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.178363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.140579 restraints weight = 28088.088| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.22 r_work: 0.3638 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21459 Z= 0.186 Angle : 0.591 7.728 29099 Z= 0.307 Chirality : 0.044 0.197 3364 Planarity : 0.004 0.056 3585 Dihedral : 11.852 172.151 3032 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.04 % Favored : 93.92 % Rotamer: Outliers : 1.64 % Allowed : 14.09 % Favored : 84.26 % 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: 0.14 (0.17), residues: 2516 helix: 1.16 (0.15), residues: 1180 sheet: -0.00 (0.24), residues: 489 loop : -1.33 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 155 TYR 0.014 0.002 TYR A 487 PHE 0.019 0.002 PHE F 160 TRP 0.009 0.002 TRP D 295 HIS 0.007 0.001 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (21459) covalent geometry : angle 0.59075 / 0.31 (29099) hydrogen bonds : bond 0.04177 / 2.72 ( 1017) hydrogen bonds : angle 4.89944 / 3.42 ( 2952) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 265 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 CYS cc_start: 0.7436 (m) cc_final: 0.7187 (m) REVERT: C 50 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8330 (tp) REVERT: C 77 ASN cc_start: 0.8060 (t0) cc_final: 0.7840 (t0) REVERT: D 115 ARG cc_start: 0.7564 (mtp85) cc_final: 0.7217 (mtm-85) REVERT: D 123 LYS cc_start: 0.8081 (pttp) cc_final: 0.7878 (tppt) REVERT: E 71 ASP cc_start: 0.7652 (p0) cc_final: 0.7404 (p0) REVERT: E 95 GLU cc_start: 0.7612 (tp30) cc_final: 0.7383 (tp30) REVERT: E 216 LYS cc_start: 0.7899 (mttm) cc_final: 0.7538 (mptt) REVERT: F 241 GLU cc_start: 0.7043 (mp0) cc_final: 0.6092 (mp0) REVERT: G 36 ASP cc_start: 0.7782 (m-30) cc_final: 0.7521 (m-30) REVERT: G 121 PHE cc_start: 0.7018 (m-80) cc_final: 0.6656 (m-80) outliers start: 38 outliers final: 27 residues processed: 291 average time/residue: 0.1449 time to fit residues: 65.1915 Evaluate side-chains 264 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 149 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 43 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 239 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 247 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS E 110 GLN G 53 ASN G 88 HIS ** H 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 363 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.179430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.141404 restraints weight = 27657.912| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.35 r_work: 0.3653 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21459 Z= 0.130 Angle : 0.536 8.395 29099 Z= 0.278 Chirality : 0.041 0.202 3364 Planarity : 0.003 0.053 3585 Dihedral : 11.767 171.478 3032 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.56 % Allowed : 15.39 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.17), residues: 2516 helix: 1.22 (0.15), residues: 1183 sheet: -0.07 (0.24), residues: 493 loop : -1.30 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 411 TYR 0.017 0.001 TYR E 8 PHE 0.013 0.001 PHE F 160 TRP 0.010 0.001 TRP C 256 HIS 0.004 0.001 HIS G 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (21459) covalent geometry : angle 0.53627 / 0.28 (29099) hydrogen bonds : bond 0.03666 / 2.39 ( 1017) hydrogen bonds : angle 4.76819 / 3.33 ( 2952) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 249 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 ASN cc_start: 0.7809 (t0) cc_final: 0.7485 (m-40) REVERT: A 403 CYS cc_start: 0.7379 (m) cc_final: 0.7142 (m) REVERT: C 50 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8315 (tp) REVERT: C 77 ASN cc_start: 0.8060 (t0) cc_final: 0.7847 (t0) REVERT: E 71 ASP cc_start: 0.7680 (p0) cc_final: 0.7461 (p0) REVERT: E 95 GLU cc_start: 0.7638 (tp30) cc_final: 0.7410 (tp30) REVERT: E 169 MET cc_start: 0.8772 (ptp) cc_final: 0.8522 (mtm) REVERT: E 216 LYS cc_start: 0.7946 (mttm) cc_final: 0.7598 (mptt) REVERT: F 241 GLU cc_start: 0.7047 (mp0) cc_final: 0.6135 (mp0) REVERT: G 155 GLU cc_start: 0.8088 (pp20) cc_final: 0.7681 (pt0) REVERT: G 185 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7591 (mm-30) outliers start: 36 outliers final: 28 residues processed: 273 average time/residue: 0.1477 time to fit residues: 61.3610 Evaluate side-chains 263 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 305 HIS Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 149 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 204 optimal weight: 5.9990 chunk 210 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 ASN ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 HIS ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS D 342 GLN E 244 ASN ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.176692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.138453 restraints weight = 27769.314| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.33 r_work: 0.3614 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21459 Z= 0.172 Angle : 0.565 8.512 29099 Z= 0.292 Chirality : 0.042 0.201 3364 Planarity : 0.004 0.054 3585 Dihedral : 11.794 171.702 3032 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.03 % Allowed : 15.87 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.17), residues: 2516 helix: 1.11 (0.15), residues: 1192 sheet: -0.20 (0.24), residues: 493 loop : -1.37 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 155 TYR 0.016 0.001 TYR E 8 PHE 0.017 0.002 PHE F 160 TRP 0.009 0.001 TRP D 324 HIS 0.035 0.001 HIS D 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (21459) covalent geometry : angle 0.56534 / 0.29 (29099) hydrogen bonds : bond 0.03934 / 2.57 ( 1017) hydrogen bonds : angle 4.76145 / 3.32 ( 2952) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 248 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7330 (pt0) REVERT: A 366 ASN cc_start: 0.7976 (t0) cc_final: 0.7720 (m-40) REVERT: A 403 CYS cc_start: 0.7328 (m) cc_final: 0.7113 (m) REVERT: B 294 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7768 (mt) REVERT: C 50 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8395 (tp) REVERT: C 195 LYS cc_start: 0.7766 (mmtm) cc_final: 0.7457 (mmtt) REVERT: E 6 ASP cc_start: 0.8404 (m-30) cc_final: 0.8149 (m-30) REVERT: E 216 LYS cc_start: 0.7954 (mttm) cc_final: 0.7604 (mptt) REVERT: F 241 GLU cc_start: 0.7065 (mp0) cc_final: 0.6289 (mp0) REVERT: G 121 PHE cc_start: 0.7404 (m-80) cc_final: 0.7089 (m-80) REVERT: G 155 GLU cc_start: 0.8207 (pp20) cc_final: 0.7751 (pt0) REVERT: G 185 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7612 (mm-30) outliers start: 47 outliers final: 35 residues processed: 282 average time/residue: 0.1470 time to fit residues: 63.9449 Evaluate side-chains 271 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 233 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 149 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 84 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 245 optimal weight: 0.1980 chunk 120 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 chunk 156 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 HIS C 77 ASN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 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 = 0.4212 r_free = 0.4212 target = 0.177427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133225 restraints weight = 27654.551| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.67 r_work: 0.3575 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21459 Z= 0.116 Angle : 0.523 9.020 29099 Z= 0.270 Chirality : 0.041 0.204 3364 Planarity : 0.003 0.053 3585 Dihedral : 11.707 171.115 3032 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.08 % Allowed : 16.21 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.17), residues: 2516 helix: 1.27 (0.16), residues: 1188 sheet: -0.17 (0.24), residues: 491 loop : -1.33 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 155 TYR 0.016 0.001 TYR C 75 PHE 0.018 0.001 PHE G 31 TRP 0.011 0.001 TRP C 256 HIS 0.006 0.001 HIS D 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (21459) covalent geometry : angle 0.52296 / 0.27 (29099) hydrogen bonds : bond 0.03467 / 2.26 ( 1017) hydrogen bonds : angle 4.65489 / 3.24 ( 2952) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 244 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7181 (pt0) REVERT: A 403 CYS cc_start: 0.7153 (m) cc_final: 0.6915 (m) REVERT: A 475 HIS cc_start: 0.5546 (OUTLIER) cc_final: 0.4355 (m90) REVERT: B 294 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7520 (mt) REVERT: C 50 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8189 (tp) REVERT: C 195 LYS cc_start: 0.7602 (mmtm) cc_final: 0.7297 (mmtt) REVERT: D 335 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7486 (t0) REVERT: E 6 ASP cc_start: 0.8429 (m-30) cc_final: 0.7990 (m-30) REVERT: E 71 ASP cc_start: 0.7937 (p0) cc_final: 0.7723 (t70) REVERT: E 216 LYS cc_start: 0.7895 (mttm) cc_final: 0.7494 (mptt) REVERT: F 241 GLU cc_start: 0.6961 (mp0) cc_final: 0.6237 (mp0) REVERT: G 36 ASP cc_start: 0.7664 (m-30) cc_final: 0.7321 (m-30) REVERT: G 121 PHE cc_start: 0.7302 (m-80) cc_final: 0.6978 (m-80) REVERT: G 155 GLU cc_start: 0.8190 (pp20) cc_final: 0.7699 (pt0) REVERT: G 185 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7695 (mm-30) outliers start: 48 outliers final: 36 residues processed: 277 average time/residue: 0.1456 time to fit residues: 62.4353 Evaluate side-chains 267 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 149 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 139 optimal weight: 0.5980 chunk 239 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 50 optimal weight: 0.0770 chunk 8 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 HIS ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 ASN ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 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 = 0.4194 r_free = 0.4194 target = 0.175640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.131930 restraints weight = 27141.574| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.56 r_work: 0.3571 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21459 Z= 0.132 Angle : 0.547 9.509 29099 Z= 0.281 Chirality : 0.041 0.203 3364 Planarity : 0.003 0.054 3585 Dihedral : 11.708 171.213 3032 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.12 % Allowed : 16.77 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2516 helix: 1.25 (0.15), residues: 1188 sheet: -0.22 (0.24), residues: 491 loop : -1.33 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 155 TYR 0.014 0.001 TYR C 75 PHE 0.027 0.001 PHE A 279 TRP 0.009 0.001 TRP D 324 HIS 0.003 0.001 HIS E 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (21459) covalent geometry : angle 0.54678 / 0.28 (29099) hydrogen bonds : bond 0.03550 / 2.31 ( 1017) hydrogen bonds : angle 4.63039 / 3.22 ( 2952) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 236 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7198 (pt0) REVERT: A 403 CYS cc_start: 0.7161 (m) cc_final: 0.6961 (m) REVERT: A 475 HIS cc_start: 0.5602 (OUTLIER) cc_final: 0.4373 (m90) REVERT: B 294 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7554 (mt) REVERT: C 50 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8232 (tp) REVERT: C 195 LYS cc_start: 0.7596 (mmtm) cc_final: 0.7299 (mmtt) REVERT: D 335 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7476 (t0) REVERT: E 6 ASP cc_start: 0.8406 (m-30) cc_final: 0.7991 (m-30) REVERT: E 216 LYS cc_start: 0.7870 (mttm) cc_final: 0.7465 (mptt) REVERT: F 241 GLU cc_start: 0.7076 (mp0) cc_final: 0.6283 (mp0) REVERT: G 121 PHE cc_start: 0.7329 (m-80) cc_final: 0.6889 (m-80) REVERT: G 155 GLU cc_start: 0.8222 (pp20) cc_final: 0.7745 (pt0) REVERT: G 185 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7567 (mm-30) REVERT: H 268 LYS cc_start: 0.7895 (tppt) cc_final: 0.6721 (tttm) outliers start: 49 outliers final: 38 residues processed: 270 average time/residue: 0.1429 time to fit residues: 60.2656 Evaluate side-chains 269 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 261 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 144 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 182 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 HIS ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS F 203 HIS ** H 243 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 = 0.4172 r_free = 0.4172 target = 0.173504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.128986 restraints weight = 27609.403| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.64 r_work: 0.3520 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21459 Z= 0.176 Angle : 0.582 9.213 29099 Z= 0.300 Chirality : 0.043 0.204 3364 Planarity : 0.004 0.054 3585 Dihedral : 11.769 171.579 3032 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.16 % Allowed : 17.12 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.17), residues: 2516 helix: 1.12 (0.15), residues: 1188 sheet: -0.31 (0.23), residues: 498 loop : -1.37 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 283 TYR 0.017 0.001 TYR C 75 PHE 0.018 0.002 PHE H 240 TRP 0.010 0.001 TRP E 259 HIS 0.004 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (21459) covalent geometry : angle 0.58228 / 0.30 (29099) hydrogen bonds : bond 0.03913 / 2.54 ( 1017) hydrogen bonds : angle 4.71731 / 3.28 ( 2952) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 239 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7280 (pt0) REVERT: A 403 CYS cc_start: 0.7202 (m) cc_final: 0.6975 (m) REVERT: B 294 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7578 (mt) REVERT: C 195 LYS cc_start: 0.7639 (mmtm) cc_final: 0.7343 (mmtt) REVERT: D 335 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7561 (t0) REVERT: E 71 ASP cc_start: 0.7921 (p0) cc_final: 0.7693 (t0) REVERT: E 216 LYS cc_start: 0.7923 (mttm) cc_final: 0.7508 (mptt) REVERT: F 241 GLU cc_start: 0.7043 (mp0) cc_final: 0.6287 (mp0) REVERT: G 121 PHE cc_start: 0.7418 (m-80) cc_final: 0.7038 (m-80) REVERT: G 135 TYR cc_start: 0.8581 (m-80) cc_final: 0.8225 (m-80) REVERT: G 155 GLU cc_start: 0.8266 (pp20) cc_final: 0.7756 (pt0) REVERT: G 185 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7639 (mm-30) REVERT: H 268 LYS cc_start: 0.7955 (tppt) cc_final: 0.6742 (tttm) outliers start: 50 outliers final: 37 residues processed: 276 average time/residue: 0.1535 time to fit residues: 66.6342 Evaluate side-chains 270 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 230 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 202 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 145 optimal weight: 8.9990 chunk 236 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 167 optimal weight: 0.4980 chunk 55 optimal weight: 0.5980 chunk 140 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 ASN G 88 HIS ** H 243 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 = 0.4189 r_free = 0.4189 target = 0.175207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.130997 restraints weight = 27560.442| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.63 r_work: 0.3550 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21459 Z= 0.126 Angle : 0.553 9.733 29099 Z= 0.286 Chirality : 0.041 0.206 3364 Planarity : 0.003 0.053 3585 Dihedral : 11.709 171.060 3032 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.77 % Allowed : 17.90 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.17), residues: 2516 helix: 1.22 (0.15), residues: 1191 sheet: -0.28 (0.23), residues: 493 loop : -1.34 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 199 TYR 0.018 0.001 TYR C 75 PHE 0.024 0.001 PHE A 364 TRP 0.012 0.001 TRP A 208 HIS 0.005 0.001 HIS G 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (21459) covalent geometry : angle 0.55315 / 0.29 (29099) hydrogen bonds : bond 0.03507 / 2.27 ( 1017) hydrogen bonds : angle 4.62912 / 3.22 ( 2952) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 247 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7230 (pt0) REVERT: A 256 MET cc_start: 0.7736 (ptp) cc_final: 0.7099 (pmm) REVERT: A 403 CYS cc_start: 0.7111 (m) cc_final: 0.6898 (m) REVERT: B 294 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7529 (mt) REVERT: C 195 LYS cc_start: 0.7610 (mmtm) cc_final: 0.7323 (mmtt) REVERT: D 335 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7444 (t0) REVERT: E 216 LYS cc_start: 0.7926 (mttm) cc_final: 0.7501 (mptt) REVERT: F 241 GLU cc_start: 0.7007 (mp0) cc_final: 0.6222 (mp0) REVERT: G 36 ASP cc_start: 0.7608 (m-30) cc_final: 0.7265 (m-30) REVERT: G 121 PHE cc_start: 0.7438 (m-80) cc_final: 0.7064 (m-80) REVERT: G 155 GLU cc_start: 0.8251 (pp20) cc_final: 0.7740 (pt0) REVERT: G 185 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7630 (mm-30) REVERT: H 268 LYS cc_start: 0.7950 (tppt) cc_final: 0.6732 (tttm) outliers start: 41 outliers final: 34 residues processed: 278 average time/residue: 0.1537 time to fit residues: 66.5146 Evaluate side-chains 267 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 230 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 55 optimal weight: 0.2980 chunk 196 optimal weight: 30.0000 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 155 optimal weight: 0.0570 chunk 118 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 171 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN G 88 HIS ** H 243 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 = 0.4187 r_free = 0.4187 target = 0.174991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.131373 restraints weight = 27212.792| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.58 r_work: 0.3561 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21459 Z= 0.120 Angle : 0.546 9.014 29099 Z= 0.282 Chirality : 0.041 0.206 3364 Planarity : 0.003 0.053 3585 Dihedral : 11.666 170.982 3032 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.73 % Allowed : 17.94 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2516 helix: 1.27 (0.15), residues: 1191 sheet: -0.28 (0.23), residues: 497 loop : -1.33 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 199 TYR 0.014 0.001 TYR C 75 PHE 0.020 0.001 PHE A 364 TRP 0.021 0.001 TRP E 4 HIS 0.006 0.001 HIS G 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (21459) covalent geometry : angle 0.54636 / 0.28 (29099) hydrogen bonds : bond 0.03370 / 2.19 ( 1017) hydrogen bonds : angle 4.56143 / 3.17 ( 2952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4610.84 seconds wall clock time: 80 minutes 20.61 seconds (4820.61 seconds total)