Starting phenix.real_space_refine on Thu Mar 5 09:41:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sgz_25121/03_2026/7sgz_25121.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sgz_25121/03_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_25121/03_2026/7sgz_25121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sgz_25121/03_2026/7sgz_25121.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sgz_25121/03_2026/7sgz_25121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sgz_25121/03_2026/7sgz_25121.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 4.41, per 1000 atoms: 0.21 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: 1.70 Conformation dependent library (CDL) restraints added in 959.1 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: 0.79 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: 3.90 Time building geometry restraints manager: 2.26 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=" 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 bond pdb=" C3' DA T 22 " pdb=" O3' DA T 22 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.73e+00 ... (remaining 21454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 28396 1.44 - 2.88: 544 2.88 - 4.33: 106 4.33 - 5.77: 41 5.77 - 7.21: 12 Bond angle restraints: 29099 Sorted by residual: angle pdb=" CA LYS A 296 " pdb=" CB LYS A 296 " pdb=" CG LYS A 296 " ideal model delta sigma weight residual 114.10 121.15 -7.05 2.00e+00 2.50e-01 1.24e+01 angle pdb=" N GLU C 279 " pdb=" CA GLU C 279 " pdb=" CB GLU C 279 " ideal model delta sigma weight residual 110.22 115.57 -5.35 1.54e+00 4.22e-01 1.21e+01 angle pdb=" N THR G 29 " pdb=" CA THR G 29 " pdb=" C THR G 29 " ideal model delta sigma weight residual 109.81 116.82 -7.01 2.21e+00 2.05e-01 1.01e+01 angle pdb=" C THR H 300 " pdb=" N LYS H 320 " pdb=" CA LYS H 320 " ideal model delta sigma weight residual 121.54 127.19 -5.65 1.91e+00 2.74e-01 8.75e+00 angle pdb=" CA GLY A 349 " pdb=" C GLY A 349 " pdb=" N SER A 350 " ideal model delta sigma weight residual 114.23 116.71 -2.48 8.80e-01 1.29e+00 7.91e+00 ... (remaining 29094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 12708 35.06 - 70.12: 350 70.12 - 105.19: 20 105.19 - 140.25: 1 140.25 - 175.31: 1 Dihedral angle restraints: 13080 sinusoidal: 5570 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 13077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3088 0.071 - 0.142: 269 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: 4.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.050 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 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= 0.113 Angle : 0.533 7.209 29099 Z= 0.273 Chirality : 0.040 0.354 3364 Planarity : 0.003 0.055 3585 Dihedral : 15.376 175.309 8182 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 covalent geometry : bond 0.00230 (21459) covalent geometry : angle 0.53327 (29099) hydrogen bonds : bond 0.20148 ( 1017) hydrogen bonds : angle 7.25374 ( 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 : 0.813 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: 0.1488 time to fit residues: 73.2859 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 : 0.676 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 341 HIS B 64 HIS ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 148 ASN D 305 HIS ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 HIS D 352 GLN G 52 ASN G 88 HIS H 53 GLN H 97 ASN H 208 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.178122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.140574 restraints weight = 27977.167| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.17 r_work: 0.3645 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 21459 Z= 0.258 Angle : 0.711 9.887 29099 Z= 0.367 Chirality : 0.048 0.252 3364 Planarity : 0.005 0.058 3585 Dihedral : 12.344 176.243 3076 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.00 % Rotamer: Outliers : 1.34 % Allowed : 10.68 % Favored : 87.98 % 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: -0.24 (0.17), residues: 2516 helix: 0.67 (0.15), residues: 1176 sheet: 0.15 (0.25), residues: 480 loop : -1.42 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 177 TYR 0.032 0.002 TYR F 16 PHE 0.025 0.003 PHE A 443 TRP 0.023 0.002 TRP E 4 HIS 0.014 0.002 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00609 (21459) covalent geometry : angle 0.71137 (29099) hydrogen bonds : bond 0.04972 ( 1017) hydrogen bonds : angle 5.29197 ( 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 317 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 286 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 403 CYS cc_start: 0.7759 (m) cc_final: 0.7516 (m) REVERT: C 197 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7645 (tp) REVERT: C 284 ILE cc_start: 0.8831 (tt) cc_final: 0.8489 (mp) REVERT: D 123 LYS cc_start: 0.8093 (pttp) cc_final: 0.7847 (tppt) REVERT: G 36 ASP cc_start: 0.8003 (m-30) cc_final: 0.7697 (m-30) REVERT: G 96 MET cc_start: 0.6827 (pmm) cc_final: 0.6490 (pmm) REVERT: G 181 TYR cc_start: 0.7835 (t80) cc_final: 0.7596 (t80) REVERT: H 253 LYS cc_start: 0.7302 (ttpp) cc_final: 0.6175 (mtpt) outliers start: 31 outliers final: 20 residues processed: 307 average time/residue: 0.1621 time to fit residues: 75.2808 Evaluate side-chains 265 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 25 ASP 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 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 37 VAL 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: 1.9990 chunk 200 optimal weight: 0.0770 chunk 189 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 177 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 ASN D 305 HIS ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN H 53 GLN H 208 ASN ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.180234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.141196 restraints weight = 27873.368| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.50 r_work: 0.3660 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2584 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= 0.131 Angle : 0.541 8.365 29099 Z= 0.280 Chirality : 0.041 0.170 3364 Planarity : 0.003 0.053 3585 Dihedral : 12.059 174.768 3076 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.43 % Allowed : 14.09 % Favored : 84.48 % 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: 0.09 (0.17), residues: 2516 helix: 1.07 (0.15), residues: 1179 sheet: 0.15 (0.24), residues: 482 loop : -1.38 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 246 TYR 0.015 0.001 TYR F 256 PHE 0.014 0.001 PHE F 160 TRP 0.010 0.001 TRP C 256 HIS 0.007 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00299 (21459) covalent geometry : angle 0.54082 (29099) hydrogen bonds : bond 0.03992 ( 1017) hydrogen bonds : angle 4.95270 ( 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 288 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 255 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8290 (tp) REVERT: C 284 ILE cc_start: 0.8756 (tt) cc_final: 0.8421 (mp) REVERT: D 209 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7402 (p0) REVERT: E 216 LYS cc_start: 0.7858 (mttm) cc_final: 0.7519 (mptt) REVERT: G 36 ASP cc_start: 0.7745 (m-30) cc_final: 0.7467 (m-30) REVERT: G 121 PHE cc_start: 0.7105 (m-80) cc_final: 0.6795 (m-80) outliers start: 33 outliers final: 20 residues processed: 276 average time/residue: 0.1488 time to fit residues: 63.5952 Evaluate side-chains 255 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 351 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 50 LEU Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 143 PHE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 209 ASN 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 102 SER Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 245 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 127 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 164 optimal weight: 0.3980 chunk 226 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 247 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 ASN D 338 ASN E 110 GLN E 244 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.180145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.141002 restraints weight = 27918.362| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.48 r_work: 0.3655 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21459 Z= 0.123 Angle : 0.525 8.450 29099 Z= 0.272 Chirality : 0.041 0.188 3364 Planarity : 0.003 0.054 3585 Dihedral : 11.951 174.825 3076 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.86 % Allowed : 14.96 % Favored : 83.18 % 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: 0.19 (0.17), residues: 2516 helix: 1.20 (0.15), residues: 1182 sheet: 0.06 (0.24), residues: 481 loop : -1.32 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 184 TYR 0.014 0.001 TYR E 8 PHE 0.023 0.001 PHE A 279 TRP 0.009 0.001 TRP E 4 HIS 0.005 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00284 (21459) covalent geometry : angle 0.52483 (29099) hydrogen bonds : bond 0.03631 ( 1017) hydrogen bonds : angle 4.77691 ( 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 289 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 246 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 216 LYS cc_start: 0.7850 (mttm) cc_final: 0.7510 (mptt) REVERT: F 241 GLU cc_start: 0.7047 (mp0) cc_final: 0.5164 (tp30) REVERT: G 36 ASP cc_start: 0.7783 (m-30) cc_final: 0.7479 (m-30) REVERT: G 121 PHE cc_start: 0.7091 (m-80) cc_final: 0.6852 (m-80) REVERT: G 155 GLU cc_start: 0.8075 (pp20) cc_final: 0.7688 (pt0) outliers start: 43 outliers final: 26 residues processed: 275 average time/residue: 0.1526 time to fit residues: 64.5321 Evaluate side-chains 263 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 237 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 48 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 89 VAL 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 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 G residue 61 LEU Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 323 GLU 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: 1.9990 chunk 26 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 239 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 247 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 475 HIS ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS D 335 ASN D 342 GLN E 144 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.176829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.137336 restraints weight = 27798.329| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.51 r_work: 0.3617 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21459 Z= 0.153 Angle : 0.553 8.624 29099 Z= 0.286 Chirality : 0.042 0.159 3364 Planarity : 0.004 0.054 3585 Dihedral : 12.018 175.258 3076 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.42 % Allowed : 15.52 % Favored : 82.06 % 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: 0.02 (0.17), residues: 2516 helix: 1.09 (0.15), residues: 1198 sheet: -0.16 (0.24), residues: 488 loop : -1.41 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 184 TYR 0.013 0.001 TYR G 181 PHE 0.015 0.002 PHE F 160 TRP 0.009 0.001 TRP D 324 HIS 0.005 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00362 (21459) covalent geometry : angle 0.55330 (29099) hydrogen bonds : bond 0.03852 ( 1017) hydrogen bonds : angle 4.72095 ( 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 311 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 255 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 HIS cc_start: 0.5674 (OUTLIER) cc_final: 0.4538 (m-70) REVERT: B 294 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7788 (mt) REVERT: C 195 LYS cc_start: 0.7761 (mmtm) cc_final: 0.7449 (mmtt) REVERT: E 216 LYS cc_start: 0.7889 (mttm) cc_final: 0.7506 (mptt) REVERT: F 241 GLU cc_start: 0.7151 (mp0) cc_final: 0.6329 (mp0) REVERT: F 420 LYS cc_start: 0.8305 (tttt) cc_final: 0.8024 (ptmt) REVERT: G 36 ASP cc_start: 0.8067 (m-30) cc_final: 0.7744 (m-30) REVERT: G 121 PHE cc_start: 0.7325 (m-80) cc_final: 0.6962 (m-80) REVERT: G 155 GLU cc_start: 0.8308 (pp20) cc_final: 0.7822 (pt0) outliers start: 56 outliers final: 39 residues processed: 295 average time/residue: 0.1523 time to fit residues: 69.2167 Evaluate side-chains 276 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 194 HIS 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 189 ASP Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 25 ASP 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 277 SER 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 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 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 251 ILE Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 323 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 204 optimal weight: 1.9990 chunk 210 optimal weight: 8.9990 chunk 163 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 81 optimal weight: 0.0980 chunk 124 optimal weight: 4.9990 chunk 154 optimal weight: 0.5980 chunk 206 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS E 244 ASN 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 = 0.4203 r_free = 0.4203 target = 0.176623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.132616 restraints weight = 27502.309| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.63 r_work: 0.3571 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21459 Z= 0.118 Angle : 0.524 8.464 29099 Z= 0.272 Chirality : 0.040 0.163 3364 Planarity : 0.003 0.062 3585 Dihedral : 11.923 174.814 3076 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.82 % Allowed : 17.03 % Favored : 81.15 % 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: 0.17 (0.17), residues: 2516 helix: 1.26 (0.15), residues: 1189 sheet: -0.17 (0.24), residues: 491 loop : -1.33 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 184 TYR 0.013 0.001 TYR C 52 PHE 0.025 0.001 PHE A 484 TRP 0.011 0.001 TRP C 256 HIS 0.004 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00268 (21459) covalent geometry : angle 0.52389 (29099) hydrogen bonds : bond 0.03478 ( 1017) hydrogen bonds : angle 4.63521 ( 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 291 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 249 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7459 (mt) REVERT: C 195 LYS cc_start: 0.7594 (mmtm) cc_final: 0.7288 (mmtt) REVERT: E 216 LYS cc_start: 0.7831 (mttm) cc_final: 0.7454 (mptt) REVERT: F 241 GLU cc_start: 0.7016 (mp0) cc_final: 0.6268 (mp0) REVERT: F 420 LYS cc_start: 0.8324 (tttt) cc_final: 0.7981 (ptmt) REVERT: G 36 ASP cc_start: 0.7608 (m-30) cc_final: 0.7252 (m-30) REVERT: G 121 PHE cc_start: 0.7190 (m-80) cc_final: 0.6840 (m-80) REVERT: G 155 GLU cc_start: 0.8217 (pp20) cc_final: 0.7707 (pt0) REVERT: H 268 LYS cc_start: 0.7934 (tppt) cc_final: 0.6703 (tttm) REVERT: H 286 ASN cc_start: 0.7153 (t0) cc_final: 0.5996 (m-40) outliers start: 42 outliers final: 34 residues processed: 277 average time/residue: 0.1490 time to fit residues: 64.2940 Evaluate side-chains 267 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 332 THR 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 294 LEU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 235 CYS 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 E residue 93 HIS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain F residue 43 THR 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 G residue 29 THR 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 36 THR Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 136 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 84 optimal weight: 0.8980 chunk 247 optimal weight: 0.0020 chunk 245 optimal weight: 5.9990 chunk 120 optimal weight: 0.3980 chunk 99 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 237 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 81 optimal weight: 0.0970 chunk 156 optimal weight: 5.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 269 ASN C 12 ASN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS E 244 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 = 0.4215 r_free = 0.4215 target = 0.177944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.134120 restraints weight = 27594.496| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.63 r_work: 0.3586 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21459 Z= 0.111 Angle : 0.523 8.756 29099 Z= 0.269 Chirality : 0.040 0.159 3364 Planarity : 0.003 0.061 3585 Dihedral : 11.835 174.675 3076 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.86 % Allowed : 17.42 % 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: 0.26 (0.17), residues: 2516 helix: 1.35 (0.15), residues: 1188 sheet: -0.19 (0.24), residues: 492 loop : -1.28 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 184 TYR 0.014 0.001 TYR E 8 PHE 0.027 0.001 PHE A 279 TRP 0.017 0.001 TRP E 4 HIS 0.004 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00248 (21459) covalent geometry : angle 0.52258 (29099) hydrogen bonds : bond 0.03313 ( 1017) hydrogen bonds : angle 4.54416 ( 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 276 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7497 (mt) REVERT: C 195 LYS cc_start: 0.7611 (mmtm) cc_final: 0.7302 (mmtt) REVERT: D 123 LYS cc_start: 0.8078 (tppt) cc_final: 0.7816 (pttp) REVERT: E 216 LYS cc_start: 0.7913 (mttm) cc_final: 0.7524 (mptt) REVERT: E 324 TYR cc_start: 0.7821 (m-10) cc_final: 0.7468 (m-10) REVERT: F 241 GLU cc_start: 0.7005 (mp0) cc_final: 0.6235 (mp0) REVERT: F 420 LYS cc_start: 0.8296 (tttt) cc_final: 0.7946 (ptmt) REVERT: G 36 ASP cc_start: 0.7586 (m-30) cc_final: 0.7228 (m-30) REVERT: G 121 PHE cc_start: 0.7212 (m-80) cc_final: 0.6826 (m-80) REVERT: G 155 GLU cc_start: 0.8220 (pp20) cc_final: 0.7736 (pt0) REVERT: H 268 LYS cc_start: 0.7904 (tppt) cc_final: 0.6726 (tttm) REVERT: H 286 ASN cc_start: 0.7188 (t0) cc_final: 0.5970 (m-40) outliers start: 43 outliers final: 30 residues processed: 262 average time/residue: 0.1442 time to fit residues: 59.4650 Evaluate side-chains 251 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 332 THR Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 381 LEU 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 111 PHE Chi-restraints excluded: chain C residue 235 CYS 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 E residue 93 HIS 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 G residue 29 THR Chi-restraints excluded: chain G residue 37 VAL 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 251 ILE Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 136 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 139 optimal weight: 0.6980 chunk 239 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 57 optimal weight: 0.0060 chunk 176 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 50 optimal weight: 0.0010 chunk 8 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 HIS C 12 ASN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS E 110 GLN E 244 ASN G 88 HIS ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.177321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.133820 restraints weight = 27493.147| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.60 r_work: 0.3580 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21459 Z= 0.109 Angle : 0.521 8.639 29099 Z= 0.267 Chirality : 0.040 0.149 3364 Planarity : 0.003 0.061 3585 Dihedral : 11.789 174.718 3076 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.90 % Allowed : 17.38 % 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: 0.32 (0.17), residues: 2516 helix: 1.41 (0.15), residues: 1187 sheet: -0.20 (0.24), residues: 499 loop : -1.25 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 184 TYR 0.013 0.001 TYR C 52 PHE 0.012 0.001 PHE A 364 TRP 0.014 0.001 TRP E 4 HIS 0.005 0.001 HIS G 88 Details of bonding type rmsd covalent geometry : bond 0.00246 (21459) covalent geometry : angle 0.52081 (29099) hydrogen bonds : bond 0.03220 ( 1017) hydrogen bonds : angle 4.45706 ( 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 274 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 230 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 294 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7545 (mt) REVERT: C 195 LYS cc_start: 0.7627 (mmtm) cc_final: 0.7326 (mmtt) REVERT: D 123 LYS cc_start: 0.8069 (tppt) cc_final: 0.7811 (pttp) REVERT: E 216 LYS cc_start: 0.7886 (mttm) cc_final: 0.7512 (mptt) REVERT: E 324 TYR cc_start: 0.7862 (m-10) cc_final: 0.7500 (m-10) REVERT: F 241 GLU cc_start: 0.7026 (mp0) cc_final: 0.6220 (mp0) REVERT: F 420 LYS cc_start: 0.8209 (tttt) cc_final: 0.7914 (ptmt) REVERT: G 36 ASP cc_start: 0.7572 (m-30) cc_final: 0.7217 (m-30) REVERT: G 121 PHE cc_start: 0.7344 (m-80) cc_final: 0.6992 (m-80) REVERT: G 155 GLU cc_start: 0.8224 (pp20) cc_final: 0.7736 (pt0) REVERT: H 268 LYS cc_start: 0.7928 (tppt) cc_final: 0.6784 (tttm) REVERT: H 286 ASN cc_start: 0.7263 (t0) cc_final: 0.6028 (m-40) outliers start: 44 outliers final: 34 residues processed: 261 average time/residue: 0.1464 time to fit residues: 59.6857 Evaluate side-chains 258 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 332 THR 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 294 LEU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 235 CYS 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 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 G residue 29 THR Chi-restraints excluded: chain G residue 37 VAL 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 305 VAL Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 149 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 144 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 HIS ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS ** E 18 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.171326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.127118 restraints weight = 27627.058| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.60 r_work: 0.3504 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21459 Z= 0.201 Angle : 0.605 9.324 29099 Z= 0.310 Chirality : 0.043 0.166 3364 Planarity : 0.004 0.058 3585 Dihedral : 11.969 175.554 3076 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.33 % Allowed : 16.95 % 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: 1.11 (0.15), residues: 1193 sheet: -0.27 (0.23), residues: 500 loop : -1.44 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 155 TYR 0.016 0.002 TYR H 64 PHE 0.029 0.002 PHE A 279 TRP 0.019 0.002 TRP E 4 HIS 0.006 0.001 HIS E 341 Details of bonding type rmsd covalent geometry : bond 0.00487 (21459) covalent geometry : angle 0.60478 (29099) hydrogen bonds : bond 0.04080 ( 1017) hydrogen bonds : angle 4.68331 ( 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 298 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 244 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 294 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7528 (mt) REVERT: C 195 LYS cc_start: 0.7683 (mmtm) cc_final: 0.7383 (mmtt) REVERT: D 123 LYS cc_start: 0.8128 (tppt) cc_final: 0.7866 (pttp) REVERT: E 216 LYS cc_start: 0.7975 (mttm) cc_final: 0.7567 (mptt) REVERT: E 224 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7942 (mp10) REVERT: F 241 GLU cc_start: 0.7107 (mp0) cc_final: 0.6278 (mp0) REVERT: F 420 LYS cc_start: 0.8205 (tttt) cc_final: 0.7890 (ptmt) REVERT: G 36 ASP cc_start: 0.7815 (m-30) cc_final: 0.7433 (m-30) REVERT: G 121 PHE cc_start: 0.7426 (m-80) cc_final: 0.7173 (m-80) REVERT: G 155 GLU cc_start: 0.8272 (pp20) cc_final: 0.7767 (pt0) REVERT: H 268 LYS cc_start: 0.7927 (tppt) cc_final: 0.6732 (tttm) outliers start: 54 outliers final: 45 residues processed: 282 average time/residue: 0.1470 time to fit residues: 64.6556 Evaluate side-chains 274 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 363 LEU Chi-restraints excluded: chain A residue 365 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 227 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 235 CYS 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 277 SER Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 273 GLU 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 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 6 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 135 ILE 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: 2.9990 chunk 198 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 236 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 167 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 HIS ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS E 244 ASN G 88 HIS ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.173677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.129707 restraints weight = 27605.004| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.63 r_work: 0.3537 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21459 Z= 0.129 Angle : 0.553 9.093 29099 Z= 0.285 Chirality : 0.041 0.225 3364 Planarity : 0.003 0.053 3585 Dihedral : 11.893 174.848 3076 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.82 % Allowed : 17.86 % 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: 0.09 (0.17), residues: 2516 helix: 1.23 (0.15), residues: 1191 sheet: -0.30 (0.23), residues: 498 loop : -1.38 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 184 TYR 0.015 0.001 TYR B 71 PHE 0.020 0.001 PHE A 364 TRP 0.018 0.001 TRP E 4 HIS 0.006 0.001 HIS G 88 Details of bonding type rmsd covalent geometry : bond 0.00300 (21459) covalent geometry : angle 0.55335 (29099) hydrogen bonds : bond 0.03525 ( 1017) hydrogen bonds : angle 4.56847 ( 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 277 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 235 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.7676 (ptp) cc_final: 0.7054 (pmm) REVERT: B 294 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7572 (mt) REVERT: C 195 LYS cc_start: 0.7695 (mmtm) cc_final: 0.7412 (mmtt) REVERT: C 205 MET cc_start: 0.8223 (tpp) cc_final: 0.7960 (tpp) REVERT: D 80 LYS cc_start: 0.7816 (mmmm) cc_final: 0.7596 (mmmt) REVERT: D 123 LYS cc_start: 0.8078 (tppt) cc_final: 0.7842 (pttp) REVERT: E 216 LYS cc_start: 0.7953 (mttm) cc_final: 0.7544 (mptt) REVERT: E 224 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7972 (mp10) REVERT: F 241 GLU cc_start: 0.7071 (mp0) cc_final: 0.6748 (mp0) REVERT: F 420 LYS cc_start: 0.8191 (tttt) cc_final: 0.7883 (ptmt) REVERT: G 36 ASP cc_start: 0.7642 (m-30) cc_final: 0.7272 (m-30) REVERT: G 121 PHE cc_start: 0.7428 (m-80) cc_final: 0.7125 (m-80) REVERT: G 155 GLU cc_start: 0.8272 (pp20) cc_final: 0.7765 (pt0) REVERT: H 268 LYS cc_start: 0.7919 (tppt) cc_final: 0.6730 (tttm) REVERT: H 286 ASN cc_start: 0.7168 (t0) cc_final: 0.6000 (m-40) outliers start: 42 outliers final: 37 residues processed: 264 average time/residue: 0.1484 time to fit residues: 61.2691 Evaluate side-chains 267 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 365 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 294 LEU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 171 ASN 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 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 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 323 GLU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 135 ILE 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: 0.8980 chunk 196 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 155 optimal weight: 0.0270 chunk 118 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS 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 = 0.4181 r_free = 0.4181 target = 0.173990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.130202 restraints weight = 27634.826| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.62 r_work: 0.3546 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3801 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= 0.126 Angle : 0.543 8.479 29099 Z= 0.279 Chirality : 0.041 0.160 3364 Planarity : 0.003 0.053 3585 Dihedral : 11.837 174.995 3076 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.77 % Allowed : 18.24 % Favored : 79.98 % 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: 0.12 (0.17), residues: 2516 helix: 1.28 (0.15), residues: 1190 sheet: -0.36 (0.23), residues: 497 loop : -1.35 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 73 TYR 0.014 0.001 TYR C 52 PHE 0.015 0.001 PHE A 364 TRP 0.018 0.001 TRP E 4 HIS 0.006 0.001 HIS G 88 Details of bonding type rmsd covalent geometry : bond 0.00292 (21459) covalent geometry : angle 0.54309 (29099) hydrogen bonds : bond 0.03442 ( 1017) hydrogen bonds : angle 4.51013 ( 2952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5176.73 seconds wall clock time: 89 minutes 27.67 seconds (5367.67 seconds total)