Starting phenix.real_space_refine on Wed May 21 14:02:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fs4_29413/05_2025/8fs4_29413.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fs4_29413/05_2025/8fs4_29413.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fs4_29413/05_2025/8fs4_29413.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fs4_29413/05_2025/8fs4_29413.map" model { file = "/net/cci-nas-00/data/ceres_data/8fs4_29413/05_2025/8fs4_29413.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fs4_29413/05_2025/8fs4_29413.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.028 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 55 5.49 5 Mg 4 5.21 5 S 112 5.16 5 C 13352 2.51 5 N 3657 2.21 5 O 4111 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21291 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3466 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 16, 'TRANS': 406} Chain breaks: 3 Chain: "B" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2482 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 1 Chain: "C" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2593 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain: "D" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2616 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2760 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 334} Chain breaks: 1 Chain: "F" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2184 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 8, 'TRANS': 261} Chain breaks: 10 Chain: "G" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2265 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 4, 'TRANS': 281} Chain breaks: 3 Chain: "H" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1930 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 7, 'TRANS': 229} Chain breaks: 9 Chain: "I" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 488 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 2 Chain: "J" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 151 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.40, per 1000 atoms: 0.63 Number of scatterers: 21291 At special positions: 0 Unit cell: (117.576, 136.62, 138.276, 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 112 16.00 P 55 15.00 Mg 4 11.99 O 4111 8.00 N 3657 7.00 C 13352 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: 5.46 Conformation dependent library (CDL) restraints added in 2.8 seconds 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4860 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 16 sheets defined 52.9% alpha, 14.4% beta 15 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 7.75 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.621A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 194 through 210 Processing helix chain 'A' and resid 238 through 241 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 269 through 282 Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 297 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 Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.914A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 393 through 409 removed outlier: 3.613A pdb=" N ALA A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 432 removed outlier: 4.170A pdb=" N ASN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 471 removed outlier: 3.614A pdb=" N ASP A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 483 through 498 Proline residue: A 489 - end of helix removed outlier: 3.800A pdb=" N SER A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.520A pdb=" N ILE B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.566A pdb=" N VAL B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 61 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 93 through 99 removed outlier: 3.517A pdb=" N ALA B 97 " --> pdb=" O ILE B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.854A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.807A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.522A pdb=" N ARG B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 220 through 228 removed outlier: 3.728A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.531A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 255 removed outlier: 3.570A pdb=" N SER B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.665A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.577A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 Processing helix chain 'C' and resid 58 through 71 Processing helix chain 'C' and resid 89 through 103 removed outlier: 3.861A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.718A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 4.033A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.529A pdb=" N VAL C 208 " --> pdb=" O ASP C 204 " (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 255 through 271 removed outlier: 4.065A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 4.014A pdb=" N LEU C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 312 removed outlier: 3.938A pdb=" N VAL C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 334 removed outlier: 3.720A pdb=" N GLY C 320 " --> pdb=" O ASP C 316 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 30 Processing helix chain 'D' and resid 35 through 39 removed outlier: 3.710A pdb=" N VAL D 39 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 55 removed outlier: 3.526A pdb=" N VAL D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.995A 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: 4.284A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.975A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) 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 152 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.557A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 removed outlier: 3.546A pdb=" N ARG D 183 " --> pdb=" O PRO D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.777A pdb=" N LEU D 235 " --> pdb=" O GLY D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 291 Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 296 through 311 Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.559A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.810A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.366A 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 62 Processing helix chain 'E' and resid 98 through 103 removed outlier: 7.297A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 119 removed outlier: 3.967A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS E 114 " --> pdb=" O GLN E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 removed outlier: 3.708A 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 153 through 161 removed outlier: 3.832A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 217 through 227 removed outlier: 3.531A pdb=" N ASN E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 291 Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.544A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP E 354 " --> pdb=" O MET E 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 30 removed outlier: 3.639A pdb=" N THR F 22 " --> pdb=" O LEU F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 113 removed outlier: 4.202A pdb=" N LEU F 100 " --> pdb=" O ASN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 219 Processing helix chain 'F' and resid 240 through 252 removed outlier: 4.206A pdb=" N SER F 244 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 412 through 424 Processing helix chain 'G' and resid 17 through 27 removed outlier: 4.096A pdb=" N ILE G 21 " --> pdb=" O HIS G 17 " (cutoff:3.500A) 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 86 through 97 removed outlier: 3.758A pdb=" N VAL G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 160 through 173 Processing helix chain 'G' and resid 239 through 243 Processing helix chain 'G' and resid 245 through 250 Processing helix chain 'G' and resid 321 through 329 Processing helix chain 'H' and resid 9 through 27 Processing helix chain 'H' and resid 59 through 61 No H-bonds generated for 'chain 'H' and resid 59 through 61' Processing helix chain 'H' and resid 98 through 105 removed outlier: 3.894A pdb=" N THR H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE H 104 " --> pdb=" O HIS H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 243 removed outlier: 3.876A pdb=" N LEU H 237 " --> pdb=" O ASN H 233 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE H 240 " --> pdb=" O LEU H 236 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN H 243 " --> pdb=" O ASN H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 336 removed outlier: 4.130A pdb=" N GLY H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.134A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 105 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE A 223 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 107 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 108 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA3, first strand: chain 'B' and resid 109 through 114 removed outlier: 6.133A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 186 removed outlier: 7.587A pdb=" N LYS B 185 " --> pdb=" O VAL B 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.099A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.244A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.216A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 76 removed outlier: 6.825A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASN E 141 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE E 96 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'F' and resid 91 through 92 removed outlier: 3.730A pdb=" N ILE F 465 " --> pdb=" O TRP F 69 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL F 428 " --> pdb=" O LEU F 235 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 153 through 160 Processing sheet with id=AB3, first strand: chain 'F' and resid 406 through 411 removed outlier: 4.401A pdb=" N LEU F 281 " --> pdb=" O TRP F 296 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS F 291 " --> pdb=" O GLU G 131 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU G 122 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER G 69 " --> pdb=" O SER G 14 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 79 through 85 removed outlier: 7.081A pdb=" N ASP G 36 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLU G 51 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP G 42 " --> pdb=" O GLY G 45 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY G 45 " --> pdb=" O ASP G 42 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP G 260 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 232 through 238 removed outlier: 3.590A pdb=" N ALA G 193 " --> pdb=" O TYR G 181 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU G 189 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE G 192 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR H 148 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL H 136 " --> pdb=" O TYR H 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 153 through 155 removed outlier: 3.995A pdb=" N SER H 93 " --> pdb=" O ILE H 155 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE H 353 " --> pdb=" O ASN H 228 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 284 through 289 removed outlier: 3.507A pdb=" N SER H 262 " --> pdb=" O GLU H 255 " (cutoff:3.500A) 1065 hydrogen bonds defined for protein. 3039 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 7.42 Time building geometry restraints manager: 6.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6893 1.36 - 1.50: 5704 1.50 - 1.65: 8957 1.65 - 1.80: 78 1.80 - 1.95: 90 Bond restraints: 21722 Sorted by residual: bond pdb=" N GLN D 25 " pdb=" CA GLN D 25 " ideal model delta sigma weight residual 1.455 1.487 -0.033 9.60e-03 1.09e+04 1.16e+01 bond pdb=" CG1 ILE H 335 " pdb=" CD1 ILE H 335 " ideal model delta sigma weight residual 1.513 1.390 0.123 3.90e-02 6.57e+02 9.96e+00 bond pdb=" N ILE F 121 " pdb=" CA ILE F 121 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.14e-02 7.69e+03 9.40e+00 bond pdb=" N VAL F 7 " pdb=" CA VAL F 7 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.19e-02 7.06e+03 9.24e+00 bond pdb=" N ILE F 72 " pdb=" CA ILE F 72 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.01e-02 9.80e+03 8.86e+00 ... (remaining 21717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 28440 1.63 - 3.26: 922 3.26 - 4.89: 124 4.89 - 6.52: 12 6.52 - 8.15: 3 Bond angle restraints: 29501 Sorted by residual: angle pdb=" N LYS D 30 " pdb=" CA LYS D 30 " pdb=" C LYS D 30 " ideal model delta sigma weight residual 114.31 108.23 6.08 1.29e+00 6.01e-01 2.22e+01 angle pdb=" CA LYS C 112 " pdb=" C LYS C 112 " pdb=" O LYS C 112 " ideal model delta sigma weight residual 121.72 116.94 4.78 1.18e+00 7.18e-01 1.64e+01 angle pdb=" N LEU E 242 " pdb=" CA LEU E 242 " pdb=" C LEU E 242 " ideal model delta sigma weight residual 112.72 107.84 4.88 1.28e+00 6.10e-01 1.46e+01 angle pdb=" N LYS A 291 " pdb=" CA LYS A 291 " pdb=" C LYS A 291 " ideal model delta sigma weight residual 112.89 108.27 4.62 1.24e+00 6.50e-01 1.39e+01 angle pdb=" CA PHE G 31 " pdb=" C PHE G 31 " pdb=" O PHE G 31 " ideal model delta sigma weight residual 122.64 117.99 4.65 1.25e+00 6.40e-01 1.38e+01 ... (remaining 29496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 12490 35.46 - 70.91: 633 70.91 - 106.37: 27 106.37 - 141.82: 1 141.82 - 177.28: 2 Dihedral angle restraints: 13153 sinusoidal: 5713 harmonic: 7440 Sorted by residual: dihedral pdb=" C5' ADP E 500 " pdb=" O5' ADP E 500 " pdb=" PA ADP E 500 " pdb=" O2A ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 117.28 -177.28 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 85.27 -145.27 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 61.01 -121.01 1 2.00e+01 2.50e-03 3.64e+01 ... (remaining 13150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3241 0.103 - 0.206: 177 0.206 - 0.308: 1 0.308 - 0.411: 0 0.411 - 0.514: 1 Chirality restraints: 3420 Sorted by residual: chirality pdb=" P DT I 34 " pdb=" OP1 DT I 34 " pdb=" OP2 DT I 34 " pdb=" O5' DT I 34 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" CA ILE F 121 " pdb=" N ILE F 121 " pdb=" C ILE F 121 " pdb=" CB ILE F 121 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE G 304 " pdb=" N ILE G 304 " pdb=" C ILE G 304 " pdb=" CB ILE G 304 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.22e-01 ... (remaining 3417 not shown) Planarity restraints: 3557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 336 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.62e+00 pdb=" N PRO H 337 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO H 337 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 337 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 470 " 0.186 9.50e-02 1.11e+02 8.36e-02 4.28e+00 pdb=" NE ARG F 470 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG F 470 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG F 470 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 470 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 224 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C GLU C 224 " -0.034 2.00e-02 2.50e+03 pdb=" O GLU C 224 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP C 225 " 0.012 2.00e-02 2.50e+03 ... (remaining 3554 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 73 2.45 - 3.06: 13992 3.06 - 3.67: 32655 3.67 - 4.29: 49372 4.29 - 4.90: 82708 Nonbonded interactions: 178800 Sorted by model distance: nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 1.835 2.170 nonbonded pdb=" O2B AGS D 401 " pdb="MG MG D 402 " model vdw 1.899 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 1.907 2.170 nonbonded pdb=" OG1 THR C 60 " pdb="MG MG C 402 " model vdw 2.093 2.170 nonbonded pdb=" OE1 GLU B 301 " pdb=" OH TYR C 308 " model vdw 2.201 3.040 ... (remaining 178795 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: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 53.590 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 21722 Z= 0.246 Angle : 0.654 8.148 29501 Z= 0.387 Chirality : 0.045 0.514 3420 Planarity : 0.004 0.084 3557 Dihedral : 18.513 177.279 8293 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.69 % Allowed : 27.31 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.18), residues: 2469 helix: 0.53 (0.16), residues: 1214 sheet: -0.21 (0.25), residues: 504 loop : -1.02 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 66 HIS 0.011 0.001 HIS E 18 PHE 0.012 0.001 PHE H 66 TYR 0.018 0.001 TYR G 181 ARG 0.006 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.18212 ( 1103) hydrogen bonds : angle 6.86122 ( 3115) covalent geometry : bond 0.00444 (21722) covalent geometry : angle 0.65354 (29501) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 245 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.4205 (tpt) cc_final: 0.3260 (mtt) REVERT: B 145 ASN cc_start: 0.8774 (m-40) cc_final: 0.8471 (m-40) REVERT: C 104 ARG cc_start: 0.6938 (ttp80) cc_final: 0.6738 (mtp85) REVERT: F 472 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7625 (tttp) REVERT: G 64 ARG cc_start: 0.7164 (ttm170) cc_final: 0.6703 (mtp180) REVERT: G 151 ARG cc_start: 0.6231 (tpp-160) cc_final: 0.4979 (tpt170) outliers start: 62 outliers final: 54 residues processed: 303 average time/residue: 1.1085 time to fit residues: 389.4040 Evaluate side-chains 281 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 227 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 407 CYS Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 67 GLN Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 83 CYS Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 250 ASP Chi-restraints excluded: chain H residue 256 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 366 ASN A 388 ASN A 411 ASN A 436 HIS C 333 ASN D 311 ASN D 340 HIS E 104 ASN E 243 ASN F 8 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 ASN G 190 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.212611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.157184 restraints weight = 23856.582| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.26 r_work: 0.3611 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 21722 Z= 0.159 Angle : 0.594 8.030 29501 Z= 0.312 Chirality : 0.044 0.198 3420 Planarity : 0.004 0.060 3557 Dihedral : 14.797 143.426 3307 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.26 % Allowed : 23.58 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.18), residues: 2469 helix: 0.82 (0.15), residues: 1205 sheet: -0.11 (0.24), residues: 508 loop : -0.70 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 42 HIS 0.007 0.001 HIS B 232 PHE 0.021 0.002 PHE F 104 TYR 0.017 0.002 TYR F 80 ARG 0.007 0.001 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 1103) hydrogen bonds : angle 5.03230 ( 3115) covalent geometry : bond 0.00369 (21722) covalent geometry : angle 0.59350 (29501) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 280 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7052 (t) cc_final: 0.6480 (p) REVERT: A 77 GLN cc_start: 0.7211 (mt0) cc_final: 0.6887 (mt0) REVERT: A 273 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6900 (mp) REVERT: C 39 LYS cc_start: 0.7362 (mtpp) cc_final: 0.6924 (ttmt) REVERT: C 293 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7307 (tm-30) REVERT: C 333 ASN cc_start: 0.6566 (m-40) cc_final: 0.6340 (m110) REVERT: D 123 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7260 (mttt) REVERT: E 96 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6983 (pt) REVERT: E 212 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6150 (tt0) REVERT: E 220 LYS cc_start: 0.7844 (tppp) cc_final: 0.7141 (mppt) REVERT: E 314 ASN cc_start: 0.8110 (OUTLIER) cc_final: 0.7887 (p0) REVERT: F 19 LEU cc_start: 0.7508 (tt) cc_final: 0.7260 (tp) REVERT: F 233 TYR cc_start: 0.5768 (m-80) cc_final: 0.5565 (m-80) REVERT: F 242 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.7542 (m-80) REVERT: F 472 LYS cc_start: 0.7931 (ttmm) cc_final: 0.7560 (tttp) REVERT: G 151 ARG cc_start: 0.5943 (tpp-160) cc_final: 0.4661 (tpt170) REVERT: G 176 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.6918 (pttt) outliers start: 98 outliers final: 37 residues processed: 346 average time/residue: 1.1590 time to fit residues: 465.6418 Evaluate side-chains 283 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 374 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 99 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 64 optimal weight: 0.0070 chunk 62 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 135 optimal weight: 0.9980 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 298 HIS D 352 GLN E 144 ASN F 406 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.207737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.152024 restraints weight = 24017.788| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.49 r_work: 0.3573 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 21722 Z= 0.144 Angle : 0.556 9.385 29501 Z= 0.290 Chirality : 0.042 0.205 3420 Planarity : 0.004 0.053 3557 Dihedral : 14.452 159.801 3238 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.17 % Allowed : 24.10 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 2469 helix: 1.03 (0.15), residues: 1201 sheet: -0.07 (0.24), residues: 509 loop : -0.65 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 42 HIS 0.005 0.001 HIS B 232 PHE 0.028 0.002 PHE H 324 TYR 0.016 0.001 TYR G 135 ARG 0.007 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 1103) hydrogen bonds : angle 4.67597 ( 3115) covalent geometry : bond 0.00339 (21722) covalent geometry : angle 0.55602 (29501) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 261 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7079 (t) cc_final: 0.6482 (p) REVERT: A 77 GLN cc_start: 0.7356 (mt0) cc_final: 0.7072 (mt0) REVERT: A 163 MET cc_start: 0.6786 (ttp) cc_final: 0.6422 (mtp) REVERT: A 178 MET cc_start: 0.3810 (tpt) cc_final: 0.2872 (mtt) REVERT: A 188 ASP cc_start: 0.5249 (m-30) cc_final: 0.4962 (m-30) REVERT: A 285 MET cc_start: 0.5460 (OUTLIER) cc_final: 0.5092 (ttp) REVERT: B 50 MET cc_start: 0.6788 (ppp) cc_final: 0.6362 (ppp) REVERT: B 297 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7513 (mtp) REVERT: C 39 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6789 (ttmt) REVERT: C 197 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7362 (tt) REVERT: C 293 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7284 (tm-30) REVERT: D 153 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7227 (mp) REVERT: E 95 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5732 (mt-10) REVERT: E 96 ILE cc_start: 0.6977 (OUTLIER) cc_final: 0.6646 (pt) REVERT: E 212 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.6293 (tt0) REVERT: F 19 LEU cc_start: 0.7501 (tt) cc_final: 0.7258 (tp) REVERT: F 472 LYS cc_start: 0.7889 (ttmm) cc_final: 0.7545 (tttp) REVERT: G 51 GLU cc_start: 0.7815 (tt0) cc_final: 0.7467 (tp30) REVERT: G 250 LYS cc_start: 0.7177 (tttp) cc_final: 0.6777 (tmtt) REVERT: H 236 LEU cc_start: 0.6502 (mp) cc_final: 0.6237 (pp) outliers start: 96 outliers final: 35 residues processed: 329 average time/residue: 1.0815 time to fit residues: 414.4343 Evaluate side-chains 276 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 115 optimal weight: 1.9990 chunk 98 optimal weight: 0.0980 chunk 244 optimal weight: 5.9990 chunk 243 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 245 optimal weight: 30.0000 chunk 7 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 101 optimal weight: 0.2980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 35 GLN B 98 GLN C 74 ASN C 292 ASN C 333 ASN E 336 ASN F 57 ASN G 164 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.207388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.152235 restraints weight = 24311.043| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.43 r_work: 0.3521 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 21722 Z= 0.190 Angle : 0.601 12.234 29501 Z= 0.309 Chirality : 0.043 0.239 3420 Planarity : 0.004 0.052 3557 Dihedral : 14.466 176.529 3231 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.12 % Allowed : 23.80 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2469 helix: 0.94 (0.15), residues: 1206 sheet: -0.08 (0.23), residues: 508 loop : -0.74 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 42 HIS 0.008 0.001 HIS B 232 PHE 0.025 0.002 PHE H 94 TYR 0.024 0.001 TYR C 71 ARG 0.005 0.000 ARG C 132 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 1103) hydrogen bonds : angle 4.62928 ( 3115) covalent geometry : bond 0.00461 (21722) covalent geometry : angle 0.60060 (29501) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 245 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7009 (t) cc_final: 0.6384 (p) REVERT: A 77 GLN cc_start: 0.7411 (mt0) cc_final: 0.7130 (mt0) REVERT: A 163 MET cc_start: 0.6817 (ttp) cc_final: 0.6389 (mtp) REVERT: A 256 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.6558 (mpt) REVERT: B 50 MET cc_start: 0.6890 (ppp) cc_final: 0.6487 (ppp) REVERT: B 297 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7549 (mtp) REVERT: C 39 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.6829 (ttmt) REVERT: C 77 ASN cc_start: 0.8026 (t0) cc_final: 0.7620 (t0) REVERT: C 104 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6129 (ttm110) REVERT: C 197 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7389 (tt) REVERT: C 207 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6946 (tpt170) REVERT: C 293 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7405 (tm-30) REVERT: D 40 THR cc_start: 0.8885 (p) cc_final: 0.8641 (t) REVERT: D 311 ASN cc_start: 0.8167 (t0) cc_final: 0.7870 (t0) REVERT: E 95 GLU cc_start: 0.5846 (OUTLIER) cc_final: 0.4763 (mt-10) REVERT: E 96 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6777 (pt) REVERT: E 97 THR cc_start: 0.7023 (OUTLIER) cc_final: 0.6767 (t) REVERT: E 212 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.6459 (tt0) REVERT: E 220 LYS cc_start: 0.7875 (tppp) cc_final: 0.7202 (tppt) REVERT: F 209 VAL cc_start: 0.2649 (OUTLIER) cc_final: 0.2342 (m) REVERT: F 264 LEU cc_start: 0.6320 (OUTLIER) cc_final: 0.6069 (mt) REVERT: F 472 LYS cc_start: 0.7898 (ttmm) cc_final: 0.7536 (tttp) REVERT: G 138 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7128 (mmmt) REVERT: G 176 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.6767 (ptmt) REVERT: H 236 LEU cc_start: 0.6433 (mp) cc_final: 0.6198 (pp) outliers start: 118 outliers final: 55 residues processed: 326 average time/residue: 1.1332 time to fit residues: 427.7427 Evaluate side-chains 291 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 222 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 138 LYS Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 145 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 33 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 214 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN C 298 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.206946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.152787 restraints weight = 24225.049| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.39 r_work: 0.3520 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21722 Z= 0.162 Angle : 0.578 11.321 29501 Z= 0.295 Chirality : 0.043 0.259 3420 Planarity : 0.004 0.046 3557 Dihedral : 14.326 156.282 3227 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.78 % Allowed : 24.79 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2469 helix: 1.05 (0.15), residues: 1205 sheet: -0.06 (0.23), residues: 504 loop : -0.69 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 42 HIS 0.006 0.001 HIS B 232 PHE 0.035 0.002 PHE H 324 TYR 0.025 0.001 TYR C 71 ARG 0.010 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 1103) hydrogen bonds : angle 4.49300 ( 3115) covalent geometry : bond 0.00388 (21722) covalent geometry : angle 0.57819 (29501) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 251 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7101 (t) cc_final: 0.6390 (p) REVERT: A 77 GLN cc_start: 0.7443 (mt0) cc_final: 0.7143 (mt0) REVERT: A 163 MET cc_start: 0.6855 (ttp) cc_final: 0.6413 (mtp) REVERT: A 178 MET cc_start: 0.3709 (tpt) cc_final: 0.2961 (mtt) REVERT: A 256 MET cc_start: 0.6796 (mpt) cc_final: 0.6499 (mpt) REVERT: A 403 CYS cc_start: 0.7455 (OUTLIER) cc_final: 0.6740 (m) REVERT: B 50 MET cc_start: 0.6861 (ppp) cc_final: 0.6512 (ppp) REVERT: B 149 LYS cc_start: 0.8541 (mmtm) cc_final: 0.8297 (mmtm) REVERT: C 39 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6857 (ttmt) REVERT: C 73 LYS cc_start: 0.7883 (pmtt) cc_final: 0.7414 (ptmm) REVERT: C 77 ASN cc_start: 0.8054 (t0) cc_final: 0.7667 (t0) REVERT: C 197 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7357 (tt) REVERT: C 293 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7426 (tm-30) REVERT: C 316 ASP cc_start: 0.8469 (t70) cc_final: 0.8141 (t0) REVERT: D 40 THR cc_start: 0.8764 (p) cc_final: 0.8531 (t) REVERT: E 95 GLU cc_start: 0.5670 (OUTLIER) cc_final: 0.5468 (mt-10) REVERT: E 96 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6784 (pt) REVERT: E 97 THR cc_start: 0.7076 (OUTLIER) cc_final: 0.6809 (t) REVERT: E 212 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6510 (tt0) REVERT: E 220 LYS cc_start: 0.7856 (tppp) cc_final: 0.7184 (tppt) REVERT: F 93 MET cc_start: 0.3890 (mpp) cc_final: 0.2190 (mtm) REVERT: F 264 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.6106 (mt) REVERT: F 407 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6453 (mt-10) REVERT: F 472 LYS cc_start: 0.7930 (ttmm) cc_final: 0.7619 (tttp) REVERT: G 176 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.6714 (ptmt) REVERT: G 250 LYS cc_start: 0.7180 (tttp) cc_final: 0.6748 (tmtt) REVERT: G 254 LYS cc_start: 0.5502 (OUTLIER) cc_final: 0.4881 (mtpm) REVERT: H 236 LEU cc_start: 0.6436 (mp) cc_final: 0.6194 (pp) outliers start: 110 outliers final: 55 residues processed: 328 average time/residue: 1.1576 time to fit residues: 439.2452 Evaluate side-chains 301 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 236 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 374 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 62 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 73 optimal weight: 0.2980 chunk 135 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN C 140 ASN C 298 HIS D 313 ASN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.208518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.154474 restraints weight = 23985.818| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.42 r_work: 0.3554 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21722 Z= 0.122 Angle : 0.542 11.016 29501 Z= 0.279 Chirality : 0.041 0.231 3420 Planarity : 0.004 0.072 3557 Dihedral : 14.165 137.711 3227 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.34 % Allowed : 25.75 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2469 helix: 1.28 (0.15), residues: 1204 sheet: 0.07 (0.24), residues: 499 loop : -0.59 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 42 HIS 0.006 0.001 HIS E 18 PHE 0.027 0.001 PHE H 94 TYR 0.028 0.001 TYR C 71 ARG 0.009 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 1103) hydrogen bonds : angle 4.32994 ( 3115) covalent geometry : bond 0.00280 (21722) covalent geometry : angle 0.54217 (29501) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 254 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7172 (t) cc_final: 0.6424 (p) REVERT: A 77 GLN cc_start: 0.7422 (mt0) cc_final: 0.7081 (mt0) REVERT: A 163 MET cc_start: 0.6841 (ttp) cc_final: 0.6388 (mtp) REVERT: A 178 MET cc_start: 0.3755 (tpt) cc_final: 0.2948 (mtt) REVERT: A 250 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.6354 (mmm) REVERT: A 256 MET cc_start: 0.6909 (mpt) cc_final: 0.6571 (mpt) REVERT: A 403 CYS cc_start: 0.7637 (OUTLIER) cc_final: 0.6859 (m) REVERT: B 50 MET cc_start: 0.6881 (ppp) cc_final: 0.6615 (ppp) REVERT: B 149 LYS cc_start: 0.8582 (mmtm) cc_final: 0.8345 (mmtm) REVERT: C 39 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6903 (ttmt) REVERT: C 73 LYS cc_start: 0.7902 (pmtt) cc_final: 0.7681 (ptmm) REVERT: C 77 ASN cc_start: 0.8007 (t0) cc_final: 0.7634 (t0) REVERT: C 197 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7358 (tt) REVERT: C 205 MET cc_start: 0.7837 (tpt) cc_final: 0.7515 (mmt) REVERT: C 207 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7143 (tpt170) REVERT: D 40 THR cc_start: 0.8795 (p) cc_final: 0.8495 (t) REVERT: E 96 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6620 (pt) REVERT: E 97 THR cc_start: 0.7085 (OUTLIER) cc_final: 0.6774 (t) REVERT: E 212 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6519 (tt0) REVERT: E 220 LYS cc_start: 0.7939 (tppp) cc_final: 0.7246 (mppt) REVERT: E 303 LEU cc_start: 0.8653 (tp) cc_final: 0.8437 (mt) REVERT: F 264 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6347 (mt) REVERT: F 287 GLU cc_start: 0.6354 (pm20) cc_final: 0.6091 (pp20) REVERT: F 472 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7768 (tttp) REVERT: G 51 GLU cc_start: 0.7791 (tt0) cc_final: 0.7368 (tp30) REVERT: G 66 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6590 (tt) REVERT: G 176 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6501 (ptmt) REVERT: G 250 LYS cc_start: 0.7185 (tttp) cc_final: 0.6771 (tmtt) REVERT: H 236 LEU cc_start: 0.6452 (mp) cc_final: 0.6201 (pp) outliers start: 100 outliers final: 49 residues processed: 330 average time/residue: 1.1364 time to fit residues: 433.2127 Evaluate side-chains 296 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 236 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 374 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 154 optimal weight: 3.9990 chunk 171 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 117 optimal weight: 0.2980 chunk 164 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 14 optimal weight: 0.0670 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 246 optimal weight: 0.9980 chunk 124 optimal weight: 0.0570 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN C 74 ASN C 140 ASN C 298 HIS D 313 ASN E 141 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.209940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.156738 restraints weight = 24037.577| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.38 r_work: 0.3576 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21722 Z= 0.112 Angle : 0.545 10.550 29501 Z= 0.277 Chirality : 0.041 0.290 3420 Planarity : 0.004 0.069 3557 Dihedral : 14.020 120.877 3227 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.30 % Allowed : 27.10 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.18), residues: 2469 helix: 1.41 (0.15), residues: 1203 sheet: 0.16 (0.24), residues: 506 loop : -0.46 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 42 HIS 0.004 0.001 HIS F 247 PHE 0.038 0.001 PHE H 324 TYR 0.029 0.001 TYR C 71 ARG 0.012 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 1103) hydrogen bonds : angle 4.24812 ( 3115) covalent geometry : bond 0.00251 (21722) covalent geometry : angle 0.54512 (29501) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 252 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7160 (t) cc_final: 0.6562 (t) REVERT: A 77 GLN cc_start: 0.7373 (mt0) cc_final: 0.7143 (mt0) REVERT: A 105 LEU cc_start: 0.6176 (tt) cc_final: 0.5437 (tp) REVERT: A 152 ARG cc_start: 0.5317 (OUTLIER) cc_final: 0.4879 (mtp85) REVERT: A 163 MET cc_start: 0.6896 (ttp) cc_final: 0.6364 (mtp) REVERT: A 178 MET cc_start: 0.3516 (tpt) cc_final: 0.2801 (mtt) REVERT: A 256 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.6458 (mpt) REVERT: A 403 CYS cc_start: 0.7372 (OUTLIER) cc_final: 0.6655 (m) REVERT: B 13 GLU cc_start: 0.7951 (tp30) cc_final: 0.7749 (mm-30) REVERT: B 79 ASN cc_start: 0.6431 (p0) cc_final: 0.6047 (p0) REVERT: B 149 LYS cc_start: 0.8541 (mmtm) cc_final: 0.8301 (mmtm) REVERT: C 19 TYR cc_start: 0.8667 (m-80) cc_final: 0.8430 (m-80) REVERT: C 39 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6800 (ttmt) REVERT: C 205 MET cc_start: 0.7740 (tpt) cc_final: 0.7392 (mmt) REVERT: C 207 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6872 (tpt170) REVERT: D 40 THR cc_start: 0.8788 (p) cc_final: 0.8485 (t) REVERT: D 115 ARG cc_start: 0.7518 (mtp85) cc_final: 0.7288 (mtp85) REVERT: D 116 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7593 (mp) REVERT: D 296 SER cc_start: 0.7590 (OUTLIER) cc_final: 0.6981 (p) REVERT: E 343 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7783 (tt0) REVERT: F 93 MET cc_start: 0.3483 (mpp) cc_final: 0.2274 (mtm) REVERT: F 407 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6020 (mt-10) REVERT: F 472 LYS cc_start: 0.7903 (ttmm) cc_final: 0.7628 (tttp) REVERT: G 51 GLU cc_start: 0.7752 (tt0) cc_final: 0.7341 (tp30) REVERT: G 176 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6489 (ptmt) REVERT: G 250 LYS cc_start: 0.7176 (tttp) cc_final: 0.6796 (tmtt) REVERT: G 328 MET cc_start: 0.4193 (ttm) cc_final: 0.2728 (ppp) REVERT: H 236 LEU cc_start: 0.6448 (mp) cc_final: 0.6069 (pp) REVERT: H 284 MET cc_start: 0.4305 (mmt) cc_final: 0.3585 (tpt) outliers start: 76 outliers final: 44 residues processed: 309 average time/residue: 1.1538 time to fit residues: 412.0648 Evaluate side-chains 284 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 232 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 324 PHE Chi-restraints excluded: chain H residue 374 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 142 optimal weight: 1.9990 chunk 200 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 249 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 224 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN E 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.205856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.152164 restraints weight = 24329.367| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.36 r_work: 0.3516 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21722 Z= 0.184 Angle : 0.597 9.759 29501 Z= 0.305 Chirality : 0.044 0.287 3420 Planarity : 0.004 0.060 3557 Dihedral : 14.109 116.081 3227 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.95 % Allowed : 26.70 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2469 helix: 1.20 (0.15), residues: 1204 sheet: 0.07 (0.23), residues: 508 loop : -0.54 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 42 HIS 0.007 0.001 HIS B 232 PHE 0.057 0.002 PHE H 324 TYR 0.034 0.002 TYR C 71 ARG 0.013 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 1103) hydrogen bonds : angle 4.39502 ( 3115) covalent geometry : bond 0.00446 (21722) covalent geometry : angle 0.59687 (29501) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 248 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7019 (t) cc_final: 0.6412 (t) REVERT: A 77 GLN cc_start: 0.7449 (mt0) cc_final: 0.7229 (mt0) REVERT: A 105 LEU cc_start: 0.6202 (tt) cc_final: 0.5479 (tp) REVERT: A 152 ARG cc_start: 0.5489 (OUTLIER) cc_final: 0.5145 (mtp85) REVERT: A 163 MET cc_start: 0.6784 (ttp) cc_final: 0.6243 (mtp) REVERT: A 178 MET cc_start: 0.3539 (tpt) cc_final: 0.2888 (mtt) REVERT: A 223 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7624 (mm) REVERT: A 225 GLU cc_start: 0.8359 (mp0) cc_final: 0.7665 (mp0) REVERT: A 250 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.6334 (mmm) REVERT: A 256 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6665 (mpt) REVERT: A 403 CYS cc_start: 0.7444 (OUTLIER) cc_final: 0.6754 (m) REVERT: B 131 MET cc_start: 0.7493 (mtp) cc_final: 0.7177 (mtp) REVERT: B 149 LYS cc_start: 0.8578 (mmtm) cc_final: 0.8340 (mmtm) REVERT: C 39 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6865 (ttmt) REVERT: C 207 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6969 (tpt170) REVERT: D 40 THR cc_start: 0.8784 (p) cc_final: 0.8496 (t) REVERT: E 220 LYS cc_start: 0.7895 (tppp) cc_final: 0.7232 (mppt) REVERT: E 343 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7872 (tt0) REVERT: F 1 MET cc_start: -0.0455 (ptm) cc_final: -0.0751 (ttp) REVERT: F 264 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6050 (mp) REVERT: F 407 GLU cc_start: 0.6658 (mt-10) cc_final: 0.5972 (mt-10) REVERT: F 472 LYS cc_start: 0.7909 (ttmm) cc_final: 0.7605 (tttp) REVERT: G 66 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6552 (tt) REVERT: G 138 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7015 (mmmt) REVERT: G 176 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6547 (ptmt) REVERT: G 250 LYS cc_start: 0.7169 (tttp) cc_final: 0.6778 (tmtt) REVERT: G 328 MET cc_start: 0.4329 (ttm) cc_final: 0.2789 (ppp) REVERT: H 284 MET cc_start: 0.4307 (mmt) cc_final: 0.3563 (tpt) outliers start: 91 outliers final: 52 residues processed: 318 average time/residue: 1.1621 time to fit residues: 428.9006 Evaluate side-chains 298 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 235 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 138 LYS Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 374 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 239 optimal weight: 0.0170 chunk 201 optimal weight: 0.5980 chunk 43 optimal weight: 0.0070 chunk 197 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 225 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 248 optimal weight: 0.0670 chunk 124 optimal weight: 0.8980 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN D 313 ASN G 20 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.209504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.156167 restraints weight = 24243.112| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.42 r_work: 0.3585 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21722 Z= 0.111 Angle : 0.556 11.105 29501 Z= 0.283 Chirality : 0.041 0.232 3420 Planarity : 0.004 0.064 3557 Dihedral : 14.001 112.688 3227 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.61 % Allowed : 28.22 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.18), residues: 2469 helix: 1.39 (0.15), residues: 1203 sheet: 0.18 (0.24), residues: 508 loop : -0.43 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 259 HIS 0.005 0.001 HIS E 18 PHE 0.024 0.001 PHE H 94 TYR 0.024 0.001 TYR C 71 ARG 0.011 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 1103) hydrogen bonds : angle 4.24261 ( 3115) covalent geometry : bond 0.00245 (21722) covalent geometry : angle 0.55554 (29501) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 260 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.7394 (mt0) cc_final: 0.7166 (mt0) REVERT: A 93 ASP cc_start: 0.8093 (t70) cc_final: 0.7580 (t0) REVERT: A 152 ARG cc_start: 0.5586 (OUTLIER) cc_final: 0.5012 (mtp85) REVERT: A 163 MET cc_start: 0.6783 (ttp) cc_final: 0.6323 (mtp) REVERT: A 178 MET cc_start: 0.3441 (tpt) cc_final: 0.2793 (mtt) REVERT: A 188 ASP cc_start: 0.4944 (m-30) cc_final: 0.4714 (m-30) REVERT: A 223 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7265 (mm) REVERT: A 225 GLU cc_start: 0.8279 (mp0) cc_final: 0.7565 (mp0) REVERT: A 250 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.6156 (mmm) REVERT: A 256 MET cc_start: 0.6787 (mpt) cc_final: 0.6586 (mpt) REVERT: A 403 CYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6648 (m) REVERT: A 476 SER cc_start: 0.7465 (m) cc_final: 0.7192 (m) REVERT: B 13 GLU cc_start: 0.7934 (tp30) cc_final: 0.7732 (mm-30) REVERT: B 79 ASN cc_start: 0.6373 (p0) cc_final: 0.6142 (p0) REVERT: B 149 LYS cc_start: 0.8532 (mmtm) cc_final: 0.8293 (mmtm) REVERT: C 19 TYR cc_start: 0.8667 (m-80) cc_final: 0.8421 (m-80) REVERT: C 39 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6796 (ttmt) REVERT: D 207 GLN cc_start: 0.8571 (mm110) cc_final: 0.8359 (mm110) REVERT: E 160 LYS cc_start: 0.8081 (ttpt) cc_final: 0.7525 (ptpp) REVERT: E 212 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6614 (tt0) REVERT: E 343 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7818 (tt0) REVERT: F 1 MET cc_start: -0.0386 (ptm) cc_final: -0.0755 (ttp) REVERT: F 93 MET cc_start: 0.3561 (mpp) cc_final: 0.2445 (mtm) REVERT: F 289 ASP cc_start: 0.5049 (m-30) cc_final: 0.4819 (t0) REVERT: F 407 GLU cc_start: 0.6552 (mt-10) cc_final: 0.6096 (mp0) REVERT: F 472 LYS cc_start: 0.7906 (ttmm) cc_final: 0.7618 (tttp) REVERT: G 51 GLU cc_start: 0.7758 (tt0) cc_final: 0.7387 (tp30) REVERT: G 151 ARG cc_start: 0.6225 (tpp-160) cc_final: 0.5091 (tpt170) REVERT: G 176 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6466 (ptmt) REVERT: G 250 LYS cc_start: 0.7020 (tttp) cc_final: 0.6648 (tmtt) REVERT: G 328 MET cc_start: 0.4254 (ttm) cc_final: 0.2715 (ppp) REVERT: H 284 MET cc_start: 0.4361 (mmt) cc_final: 0.3596 (tpt) outliers start: 60 outliers final: 38 residues processed: 305 average time/residue: 1.1860 time to fit residues: 416.7940 Evaluate side-chains 290 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 245 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 212 GLN Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 374 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 215 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 66 optimal weight: 0.0570 chunk 68 optimal weight: 0.5980 chunk 231 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 251 optimal weight: 8.9990 chunk 117 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 229 optimal weight: 7.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN C 292 ASN E 144 ASN E 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.207200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.154249 restraints weight = 24323.748| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.41 r_work: 0.3549 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21722 Z= 0.139 Angle : 0.575 12.512 29501 Z= 0.292 Chirality : 0.042 0.242 3420 Planarity : 0.004 0.063 3557 Dihedral : 14.000 111.401 3227 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.30 % Allowed : 28.53 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2469 helix: 1.35 (0.15), residues: 1213 sheet: 0.19 (0.24), residues: 508 loop : -0.44 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 42 HIS 0.006 0.001 HIS F 247 PHE 0.045 0.002 PHE H 324 TYR 0.038 0.001 TYR F 107 ARG 0.009 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 1103) hydrogen bonds : angle 4.27422 ( 3115) covalent geometry : bond 0.00327 (21722) covalent geometry : angle 0.57539 (29501) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 239 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7245 (t) cc_final: 0.6757 (p) REVERT: A 77 GLN cc_start: 0.7440 (mt0) cc_final: 0.7149 (mt0) REVERT: A 93 ASP cc_start: 0.8086 (t70) cc_final: 0.7572 (t0) REVERT: A 152 ARG cc_start: 0.5371 (OUTLIER) cc_final: 0.5109 (mtp85) REVERT: A 178 MET cc_start: 0.3404 (tpt) cc_final: 0.2797 (mtt) REVERT: A 223 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7429 (mm) REVERT: A 225 GLU cc_start: 0.8360 (mp0) cc_final: 0.7619 (mp0) REVERT: A 250 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.6216 (mmm) REVERT: A 256 MET cc_start: 0.6786 (OUTLIER) cc_final: 0.6575 (mpt) REVERT: A 403 CYS cc_start: 0.7421 (OUTLIER) cc_final: 0.6728 (m) REVERT: A 476 SER cc_start: 0.7476 (m) cc_final: 0.7227 (m) REVERT: B 13 GLU cc_start: 0.7949 (tp30) cc_final: 0.7736 (mm-30) REVERT: B 50 MET cc_start: 0.6777 (ppp) cc_final: 0.6423 (ppp) REVERT: B 149 LYS cc_start: 0.8548 (mmtm) cc_final: 0.8312 (mmtm) REVERT: C 39 LYS cc_start: 0.7279 (mtpp) cc_final: 0.6853 (ttmt) REVERT: D 40 THR cc_start: 0.8773 (p) cc_final: 0.8439 (t) REVERT: E 343 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7872 (tt0) REVERT: F 1 MET cc_start: -0.0319 (ptm) cc_final: -0.0673 (ttp) REVERT: F 93 MET cc_start: 0.3640 (mpp) cc_final: 0.2491 (mtm) REVERT: F 407 GLU cc_start: 0.6656 (mt-10) cc_final: 0.6268 (mp0) REVERT: F 472 LYS cc_start: 0.7915 (ttmm) cc_final: 0.7610 (tttp) REVERT: G 138 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6955 (mmmt) REVERT: G 176 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6488 (ptmt) REVERT: G 250 LYS cc_start: 0.7040 (tttp) cc_final: 0.6615 (tmtt) REVERT: G 328 MET cc_start: 0.4270 (ttm) cc_final: 0.2716 (ppp) REVERT: H 284 MET cc_start: 0.4327 (mmt) cc_final: 0.3508 (tpt) outliers start: 53 outliers final: 39 residues processed: 280 average time/residue: 1.1908 time to fit residues: 382.9355 Evaluate side-chains 280 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 295 CYS Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 138 LYS Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 374 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 219 optimal weight: 3.9990 chunk 245 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 236 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 240 optimal weight: 0.7980 chunk 233 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 188 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN C 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.206435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.153083 restraints weight = 24300.677| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.34 r_work: 0.3536 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21722 Z= 0.150 Angle : 0.587 12.098 29501 Z= 0.298 Chirality : 0.043 0.237 3420 Planarity : 0.004 0.056 3557 Dihedral : 14.059 111.103 3227 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 2.91 % Allowed : 27.83 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2469 helix: 1.31 (0.15), residues: 1206 sheet: 0.19 (0.24), residues: 508 loop : -0.49 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 42 HIS 0.006 0.001 HIS E 18 PHE 0.023 0.001 PHE H 94 TYR 0.032 0.002 TYR C 71 ARG 0.012 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 1103) hydrogen bonds : angle 4.31176 ( 3115) covalent geometry : bond 0.00357 (21722) covalent geometry : angle 0.58724 (29501) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15105.84 seconds wall clock time: 261 minutes 10.08 seconds (15670.08 seconds total)