Starting phenix.real_space_refine on Mon Mar 18 15:21:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs4_29413/03_2024/8fs4_29413_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs4_29413/03_2024/8fs4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs4_29413/03_2024/8fs4_29413.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs4_29413/03_2024/8fs4_29413.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs4_29413/03_2024/8fs4_29413_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs4_29413/03_2024/8fs4_29413_updated.pdb" } 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 Residue "A GLU 64": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E GLU 120": "OE1" <-> "OE2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "G GLU 131": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 11.05, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 8.80 Conformation dependent library (CDL) restraints added in 3.5 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... running ksdssp... Secondary structure from input PDB file: 109 helices and 16 sheets defined 45.7% alpha, 14.5% beta 15 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 8.79 Creating SS restraints... Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 117 through 130 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 165 through 171 Processing helix chain 'A' and resid 195 through 209 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 246 through 249 No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 295 through 307 removed outlier: 4.756A pdb=" N GLN A 298 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU A 299 " --> pdb=" O LYS A 296 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 300 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE A 304 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 356 through 366 Processing helix chain 'A' and resid 374 through 386 removed outlier: 5.117A pdb=" N ASN A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N THR A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 409 removed outlier: 3.518A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 removed outlier: 3.509A pdb=" N ARG A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 470 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 477 through 482 Processing helix chain 'A' and resid 484 through 497 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 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 56 through 70 removed outlier: 3.647A pdb=" N CYS B 61 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ARG B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 89 No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 93 through 98 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 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 121 through 133 removed outlier: 3.854A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 152 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 168 through 182 removed outlier: 3.522A pdb=" N ARG B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.728A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 245 through 254 Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 282 through 301 Processing helix chain 'B' and resid 306 through 321 Processing helix chain 'C' and resid 15 through 18 No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 32 through 43 Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 90 through 102 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 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 124 through 134 removed outlier: 4.546A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 241 through 253 Processing helix chain 'C' and resid 256 through 270 removed outlier: 4.065A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 316 through 333 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) Processing helix chain 'D' and resid 27 through 29 No H-bonds generated for 'chain 'D' and resid 27 through 29' Processing helix chain 'D' and resid 36 through 38 No H-bonds generated for 'chain 'D' and resid 36 through 38' Processing helix chain 'D' and resid 43 through 54 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 71 through 82 Processing helix chain 'D' and resid 85 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 103 through 115 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 123 through 128 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 147 through 159 removed outlier: 3.559A pdb=" N LEU D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 178 through 183 removed outlier: 3.546A pdb=" N ARG D 183 " --> pdb=" O PRO D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 208 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 228 through 245 removed outlier: 3.777A pdb=" N LEU D 235 " --> pdb=" O GLY D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 265 through 277 Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.787A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER D 293 " --> pdb=" O THR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 310 Processing helix chain 'D' and resid 316 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 339 through 352 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 13 through 15 No H-bonds generated for 'chain 'E' and resid 13 through 15' Processing helix chain 'E' and resid 20 through 35 removed outlier: 4.366A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Proline residue: E 33 - end of helix Processing helix chain 'E' and resid 49 through 61 Processing helix chain 'E' and resid 98 through 118 removed outlier: 7.297A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN E 104 " --> pdb=" O MET E 101 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU E 112 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU E 113 " --> pdb=" O GLN E 110 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS E 114 " --> pdb=" O GLU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 150 through 160 removed outlier: 3.648A pdb=" N ARG E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) 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 179 through 183 Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 218 through 226 Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 292 removed outlier: 3.701A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 309 removed outlier: 3.746A pdb=" N ASP E 309 " --> pdb=" O PHE E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 333 Processing helix chain 'E' and resid 338 through 353 removed outlier: 3.594A pdb=" N ILE E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 29 removed outlier: 3.639A pdb=" N THR F 22 " --> pdb=" O LEU F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 112 Processing helix chain 'F' and resid 214 through 218 Processing helix chain 'F' and resid 241 through 254 removed outlier: 4.539A pdb=" N ALA F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL F 253 " --> pdb=" O PHE F 249 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLU F 254 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 423 Processing helix chain 'G' and resid 18 through 26 Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 86 through 99 removed outlier: 3.758A pdb=" N VAL G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG G 98 " --> pdb=" O SER G 94 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN G 99 " --> pdb=" O VAL G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 172 Processing helix chain 'G' and resid 239 through 251 removed outlier: 4.013A pdb=" N LYS G 244 " --> pdb=" O THR G 240 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG G 246 " --> pdb=" O PHE G 242 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS G 247 " --> pdb=" O ASP G 243 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N SER G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE G 251 " --> pdb=" O LYS G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 328 Processing helix chain 'H' and resid 10 through 26 Processing helix chain 'H' and resid 58 through 60 No H-bonds generated for 'chain 'H' and resid 58 through 60' Processing helix chain 'H' and resid 98 through 104 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 234 through 243 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 329 through 336 removed outlier: 4.130A pdb=" N GLY H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 219 through 224 removed outlier: 3.780A pdb=" N SER A 108 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 159 through 162 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) Processing sheet with id= C, first strand: chain 'C' and resid 162 through 166 removed outlier: 3.754A pdb=" N GLY C 53 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 185 through 189 removed outlier: 3.632A pdb=" N GLY D 65 " --> pdb=" O CYS D 170 " (cutoff:3.500A) 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= E, first strand: chain 'E' and resid 186 through 190 removed outlier: 3.678A pdb=" N GLY E 43 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 3 through 5 Processing sheet with id= G, first strand: chain 'F' and resid 91 through 95 removed outlier: 3.654A pdb=" N LEU F 35 " --> pdb=" O MET F 93 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 153 through 160 Processing sheet with id= I, first strand: chain 'F' and resid 231 through 235 removed outlier: 4.670A pdb=" N VAL F 428 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER F 437 " --> pdb=" O SER F 433 " (cutoff:3.500A) Processing sheet with id= J, 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) Processing sheet with id= K, first strand: chain 'G' and resid 11 through 15 removed outlier: 3.718A pdb=" N GLU G 122 " --> pdb=" O GLU G 105 " (cutoff:3.500A) Processing sheet with id= L, 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= M, 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) Processing sheet with id= N, first strand: chain 'H' and resid 64 through 66 removed outlier: 6.918A pdb=" N GLU H 139 " --> pdb=" O LYS H 114 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE H 116 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL H 137 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE H 118 " --> pdb=" O ILE H 135 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE H 135 " --> pdb=" O ILE H 118 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL H 136 " --> pdb=" O TYR H 148 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR H 148 " --> pdb=" O VAL H 136 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 228 through 230 removed outlier: 3.669A pdb=" N PHE H 353 " --> pdb=" O ASN H 228 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER H 93 " --> pdb=" O ILE H 155 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 320 through 324 removed outlier: 3.509A pdb=" N ILE H 256 " --> pdb=" O LYS H 320 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER H 262 " --> pdb=" O GLU H 255 " (cutoff:3.500A) 921 hydrogen bonds defined for protein. 2625 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: 6.80 Time building geometry restraints manager: 9.31 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: 97.52 - 105.33: 467 105.33 - 113.13: 12320 113.13 - 120.94: 10570 120.94 - 128.74: 5991 128.74 - 136.55: 153 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: 14072 3.06 - 3.67: 32783 3.67 - 4.29: 49678 4.29 - 4.90: 82771 Nonbonded interactions: 179377 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 2.440 ... (remaining 179372 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 16.160 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 61.500 Find NCS groups from input model: 0.720 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: 0.000 Load rotamer database and sin/cos tables:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.570 ------------------------------------------------------------------------------- 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= 0.289 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 *********************** 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 fitting. rotamer outliers: 62 poor density : 245 time to evaluate : 2.107 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: 1.1207 time to fit residues: 393.3522 Evaluate side-chains 281 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 227 time to evaluate : 2.138 ------------------------------------------------------------------------------- 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: 5.9990 chunk 106 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 198 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 229 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN A 366 ASN A 411 ASN A 436 HIS C 333 ASN D 255 GLN D 311 ASN E 144 ASN E 243 ASN E 244 ASN F 8 ASN G 190 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 21722 Z= 0.219 Angle : 0.560 8.010 29501 Z= 0.294 Chirality : 0.042 0.207 3420 Planarity : 0.004 0.055 3557 Dihedral : 14.883 165.393 3307 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.47 % Allowed : 24.40 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.07 (0.18), residues: 2469 helix: 0.72 (0.16), residues: 1205 sheet: -0.12 (0.24), residues: 515 loop : -0.75 (0.23), residues: 749 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 0.018 0.002 PHE H 66 TYR 0.015 0.001 TYR F 80 ARG 0.008 0.000 ARG F 20 *********************** 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 376 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 273 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.6895 (t) cc_final: 0.6482 (p) REVERT: A 273 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6941 (mp) REVERT: B 50 MET cc_start: 0.7120 (ppp) cc_final: 0.6899 (ppp) REVERT: C 39 LYS cc_start: 0.7735 (mtpp) cc_final: 0.7519 (ttmt) REVERT: C 293 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7216 (tm-30) REVERT: D 123 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7253 (mttt) REVERT: E 212 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.6133 (tt0) REVERT: E 314 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8451 (OUTLIER) REVERT: F 19 LEU cc_start: 0.7716 (tt) cc_final: 0.7420 (tp) REVERT: F 291 HIS cc_start: 0.7590 (t70) cc_final: 0.7326 (t-90) REVERT: F 472 LYS cc_start: 0.7920 (ttmm) cc_final: 0.7584 (tttp) REVERT: G 151 ARG cc_start: 0.6327 (tpp-160) cc_final: 0.5154 (tpt170) REVERT: G 176 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7118 (pttt) REVERT: H 335 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6499 (mp) outliers start: 103 outliers final: 43 residues processed: 343 average time/residue: 1.1294 time to fit residues: 448.1325 Evaluate side-chains 289 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 241 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 108 SER 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 B residue 41 ASN 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 223 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 123 LYS 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 311 ASN Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 195 ASP 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 316 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 108 ASP 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 289 ASP Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 111 ASP 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 202 PHE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 335 ILE 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 127 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 248 optimal weight: 0.0870 chunk 204 optimal weight: 3.9990 chunk 228 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 184 optimal weight: 5.9990 overall best weight: 1.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN B 98 GLN C 180 ASN C 333 ASN D 255 GLN D 352 GLN E 45 ASN E 336 ASN F 57 ASN G 74 ASN G 190 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21722 Z= 0.242 Angle : 0.553 9.927 29501 Z= 0.286 Chirality : 0.042 0.176 3420 Planarity : 0.004 0.050 3557 Dihedral : 14.634 152.385 3245 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.25 % Allowed : 24.19 % Favored : 70.56 % 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: 0.11 (0.17), residues: 2469 helix: 0.76 (0.15), residues: 1194 sheet: -0.08 (0.23), residues: 522 loop : -0.72 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 42 HIS 0.007 0.001 HIS E 18 PHE 0.029 0.002 PHE H 324 TYR 0.022 0.001 TYR A 471 ARG 0.007 0.001 ARG C 68 *********************** 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 386 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 265 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.6939 (t) cc_final: 0.6527 (p) REVERT: A 178 MET cc_start: 0.3869 (tpt) cc_final: 0.3081 (mtt) REVERT: A 247 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6208 (pt0) REVERT: A 273 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7040 (mp) REVERT: B 272 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7597 (mmm160) REVERT: C 39 LYS cc_start: 0.7816 (mtpp) cc_final: 0.7560 (ttmt) REVERT: C 104 ARG cc_start: 0.7864 (ttm110) cc_final: 0.7284 (mtm180) REVERT: C 293 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7259 (tm-30) REVERT: D 123 LYS cc_start: 0.7808 (mttp) cc_final: 0.7490 (mttm) REVERT: E 95 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.5907 (mt-10) REVERT: E 212 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6288 (tt0) REVERT: E 314 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8500 (p0) REVERT: F 19 LEU cc_start: 0.7749 (tt) cc_final: 0.7443 (tp) REVERT: F 472 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7642 (tttp) REVERT: G 151 ARG cc_start: 0.6428 (tpp-160) cc_final: 0.5272 (tpt170) REVERT: G 189 GLU cc_start: 0.5480 (OUTLIER) cc_final: 0.5278 (mp0) outliers start: 121 outliers final: 54 residues processed: 345 average time/residue: 1.1446 time to fit residues: 456.9106 Evaluate side-chains 297 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 236 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 66 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 B residue 227 ILE Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 70 ILE 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 69 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 135 LYS 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 311 ASN Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 195 ASP 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 314 ASN 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 212 LEU Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 374 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 227 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 244 optimal weight: 0.4980 chunk 120 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN B 146 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS D 255 GLN G 164 HIS G 190 ASN ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21722 Z= 0.305 Angle : 0.588 11.969 29501 Z= 0.303 Chirality : 0.043 0.154 3420 Planarity : 0.004 0.047 3557 Dihedral : 14.676 150.902 3239 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.69 % Allowed : 24.84 % Favored : 69.47 % 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: -0.01 (0.17), residues: 2469 helix: 0.61 (0.15), residues: 1194 sheet: -0.05 (0.23), residues: 522 loop : -0.77 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 42 HIS 0.008 0.001 HIS B 232 PHE 0.024 0.002 PHE H 94 TYR 0.024 0.002 TYR C 71 ARG 0.014 0.001 ARG C 132 *********************** 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 371 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 240 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.6958 (t) cc_final: 0.6510 (p) REVERT: A 152 ARG cc_start: 0.5865 (OUTLIER) cc_final: 0.4797 (mtp85) REVERT: A 247 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6310 (pt0) REVERT: A 273 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7132 (mp) REVERT: A 365 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7987 (pt0) REVERT: A 403 CYS cc_start: 0.7454 (OUTLIER) cc_final: 0.6964 (m) REVERT: B 129 ARG cc_start: 0.7660 (tpm170) cc_final: 0.7343 (tpm170) REVERT: B 272 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7636 (mmm160) REVERT: B 297 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7404 (mtp) REVERT: C 39 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7596 (ttmt) REVERT: C 77 ASN cc_start: 0.7820 (t0) cc_final: 0.7429 (t0) REVERT: C 132 ARG cc_start: 0.7793 (tpt90) cc_final: 0.7498 (tpt170) REVERT: C 207 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7169 (tpt170) REVERT: C 293 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7347 (tm-30) REVERT: D 153 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7857 (mp) REVERT: E 95 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5823 (mt-10) REVERT: E 103 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7896 (t0) REVERT: E 212 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6484 (tt0) REVERT: E 220 LYS cc_start: 0.8107 (tppp) cc_final: 0.7545 (mppt) REVERT: E 314 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8524 (p0) REVERT: F 209 VAL cc_start: 0.2906 (OUTLIER) cc_final: 0.2626 (m) REVERT: F 472 LYS cc_start: 0.8111 (ttmm) cc_final: 0.7762 (tttp) REVERT: G 176 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.6886 (ptmt) REVERT: G 189 GLU cc_start: 0.5476 (OUTLIER) cc_final: 0.5269 (mp0) REVERT: G 254 LYS cc_start: 0.5902 (OUTLIER) cc_final: 0.5224 (mttm) outliers start: 131 outliers final: 61 residues processed: 334 average time/residue: 1.1135 time to fit residues: 430.5965 Evaluate side-chains 301 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 222 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 404 LEU 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 79 ASN Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 272 ARG 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 207 ARG 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 117 THR Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain D residue 153 LEU 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 311 ASN Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 195 ASP 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 248 LEU Chi-restraints excluded: chain E residue 314 ASN 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 101 LEU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 212 LEU 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 111 ASP 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 189 GLU 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 254 LYS Chi-restraints excluded: chain G residue 312 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 331 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 203 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 100 optimal weight: 0.0060 chunk 208 optimal weight: 0.0570 chunk 169 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 124 optimal weight: 0.0970 chunk 219 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.3712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN A 388 ASN B 146 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS D 255 GLN G 190 ASN ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21722 Z= 0.151 Angle : 0.520 10.252 29501 Z= 0.266 Chirality : 0.040 0.251 3420 Planarity : 0.003 0.041 3557 Dihedral : 14.473 130.253 3237 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.96 % Favored : 97.00 % Rotamer: Outliers : 4.26 % Allowed : 26.79 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.41 (0.18), residues: 2469 helix: 1.01 (0.16), residues: 1190 sheet: 0.08 (0.23), residues: 519 loop : -0.60 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 42 HIS 0.005 0.001 HIS E 18 PHE 0.032 0.001 PHE H 324 TYR 0.022 0.001 TYR F 107 ARG 0.008 0.000 ARG C 68 *********************** 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 344 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 246 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.6934 (t) cc_final: 0.6415 (p) REVERT: A 152 ARG cc_start: 0.5854 (OUTLIER) cc_final: 0.4559 (mtp85) REVERT: A 178 MET cc_start: 0.3726 (tpt) cc_final: 0.3183 (mtt) REVERT: A 247 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6273 (pt0) REVERT: A 251 ASN cc_start: 0.6554 (p0) cc_final: 0.6251 (p0) REVERT: A 403 CYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6909 (m) REVERT: B 297 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.7291 (mtp) REVERT: C 39 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7582 (ttmt) REVERT: C 73 LYS cc_start: 0.7788 (pmtt) cc_final: 0.7456 (ptmm) REVERT: C 77 ASN cc_start: 0.7543 (t0) cc_final: 0.7313 (t0) REVERT: C 132 ARG cc_start: 0.7650 (tpt90) cc_final: 0.7382 (tpt170) REVERT: E 93 HIS cc_start: 0.7012 (p-80) cc_final: 0.6744 (p-80) REVERT: E 212 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6445 (tt0) REVERT: E 314 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8516 (OUTLIER) REVERT: F 472 LYS cc_start: 0.8107 (ttmm) cc_final: 0.7810 (tttp) REVERT: G 176 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.6818 (ptmt) REVERT: G 250 LYS cc_start: 0.7452 (tttp) cc_final: 0.7022 (tmtt) outliers start: 98 outliers final: 47 residues processed: 322 average time/residue: 1.1663 time to fit residues: 436.5207 Evaluate side-chains 283 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 229 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 301 GLU 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 57 THR Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 104 ASN 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 314 ASN Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 334 LEU 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 108 ASP Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 111 ASP 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 312 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 145 VAL 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 82 optimal weight: 0.9990 chunk 220 optimal weight: 0.0020 chunk 48 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 60 optimal weight: 0.4980 chunk 244 optimal weight: 30.0000 chunk 203 optimal weight: 0.0270 chunk 113 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.3646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN A 388 ASN B 146 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21722 Z= 0.150 Angle : 0.508 10.097 29501 Z= 0.258 Chirality : 0.040 0.227 3420 Planarity : 0.003 0.046 3557 Dihedral : 14.297 124.897 3235 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.00 % Favored : 96.96 % Rotamer: Outliers : 4.04 % Allowed : 27.23 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.61 (0.18), residues: 2469 helix: 1.18 (0.16), residues: 1189 sheet: 0.16 (0.24), residues: 521 loop : -0.52 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 42 HIS 0.004 0.001 HIS E 18 PHE 0.029 0.001 PHE A 279 TYR 0.014 0.001 TYR G 135 ARG 0.009 0.000 ARG C 68 *********************** 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 326 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 233 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.6968 (t) cc_final: 0.6449 (p) REVERT: A 178 MET cc_start: 0.3773 (OUTLIER) cc_final: 0.3145 (mtt) REVERT: A 247 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6311 (pt0) REVERT: A 273 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6939 (mp) REVERT: A 403 CYS cc_start: 0.7398 (OUTLIER) cc_final: 0.6882 (m) REVERT: B 50 MET cc_start: 0.7153 (ppp) cc_final: 0.6929 (ppp) REVERT: B 297 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7290 (mtp) REVERT: C 39 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7572 (ttmt) REVERT: C 91 ASP cc_start: 0.7503 (m-30) cc_final: 0.7234 (m-30) REVERT: E 165 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7658 (tt) REVERT: E 314 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8509 (OUTLIER) REVERT: F 407 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6022 (mt-10) REVERT: F 472 LYS cc_start: 0.8071 (ttmm) cc_final: 0.7781 (tttp) REVERT: G 176 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.6768 (ptmt) outliers start: 93 outliers final: 52 residues processed: 306 average time/residue: 1.1868 time to fit residues: 419.6706 Evaluate side-chains 283 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 223 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 353 THR 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 41 ASN Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 301 GLU 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 78 MET Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 125 ASP 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 311 ASN Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 218 ILE 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 334 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 111 ASP 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 249 THR Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 312 GLU 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 374 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 236 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 243 optimal weight: 30.0000 chunk 152 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 146 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21722 Z= 0.236 Angle : 0.550 9.321 29501 Z= 0.279 Chirality : 0.042 0.203 3420 Planarity : 0.004 0.040 3557 Dihedral : 14.285 130.102 3233 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.20 % Favored : 96.76 % Rotamer: Outliers : 4.69 % Allowed : 26.79 % Favored : 68.52 % 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: 0.47 (0.18), residues: 2469 helix: 1.02 (0.15), residues: 1188 sheet: 0.16 (0.23), residues: 521 loop : -0.55 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 42 HIS 0.007 0.001 HIS E 93 PHE 0.040 0.001 PHE H 324 TYR 0.015 0.001 TYR A 67 ARG 0.010 0.000 ARG C 68 *********************** 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 347 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 239 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.6993 (t) cc_final: 0.6449 (p) REVERT: A 178 MET cc_start: 0.3711 (OUTLIER) cc_final: 0.3240 (mtt) REVERT: A 195 ILE cc_start: 0.6575 (mm) cc_final: 0.4538 (mm) REVERT: A 199 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6371 (mtt90) REVERT: A 247 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6254 (pt0) REVERT: A 250 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.6260 (mmm) REVERT: A 273 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6921 (mp) REVERT: A 403 CYS cc_start: 0.7426 (OUTLIER) cc_final: 0.6927 (m) REVERT: B 50 MET cc_start: 0.7289 (ppp) cc_final: 0.7060 (ppp) REVERT: B 131 MET cc_start: 0.7690 (mtp) cc_final: 0.7422 (mtp) REVERT: B 297 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7389 (mtp) REVERT: C 39 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7570 (ttmt) REVERT: C 73 LYS cc_start: 0.7801 (pmtt) cc_final: 0.7412 (ptmm) REVERT: C 77 ASN cc_start: 0.7738 (t0) cc_final: 0.7493 (t0) REVERT: E 95 GLU cc_start: 0.5798 (OUTLIER) cc_final: 0.5594 (mt-10) REVERT: E 160 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7768 (ptpp) REVERT: E 165 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7807 (tt) REVERT: E 220 LYS cc_start: 0.8143 (tppp) cc_final: 0.7621 (mppt) REVERT: E 314 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8512 (p0) REVERT: E 343 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7961 (tt0) REVERT: F 119 MET cc_start: 0.2965 (ptt) cc_final: 0.2231 (ptp) REVERT: F 289 ASP cc_start: 0.4949 (OUTLIER) cc_final: 0.4734 (t0) REVERT: F 407 GLU cc_start: 0.6664 (mt-10) cc_final: 0.6013 (mt-10) REVERT: F 472 LYS cc_start: 0.8055 (ttmm) cc_final: 0.7768 (tttp) REVERT: G 176 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.6780 (ptmt) REVERT: G 250 LYS cc_start: 0.7435 (tttp) cc_final: 0.7018 (tmtt) REVERT: G 328 MET cc_start: 0.4382 (ttm) cc_final: 0.2814 (ppp) REVERT: H 284 MET cc_start: 0.4317 (mmt) cc_final: 0.3573 (tpt) outliers start: 108 outliers final: 57 residues processed: 319 average time/residue: 1.1903 time to fit residues: 435.6299 Evaluate side-chains 296 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 226 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 353 THR 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 A residue 490 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 297 MET 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 70 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 96 ASN 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 311 ASN Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 165 ILE 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 314 ASN 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 334 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 289 ASP 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 111 ASP 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 249 THR Chi-restraints excluded: chain G residue 269 ILE Chi-restraints excluded: chain G residue 312 GLU 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 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 150 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 155 optimal weight: 0.0470 chunk 166 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 221 optimal weight: 9.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 146 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21722 Z= 0.243 Angle : 0.557 10.983 29501 Z= 0.282 Chirality : 0.042 0.209 3420 Planarity : 0.004 0.043 3557 Dihedral : 14.208 135.580 3233 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.24 % Favored : 96.72 % Rotamer: Outliers : 4.26 % Allowed : 27.40 % Favored : 68.35 % 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: 0.93 (0.15), residues: 1198 sheet: 0.10 (0.23), residues: 527 loop : -0.60 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 42 HIS 0.008 0.001 HIS E 18 PHE 0.045 0.002 PHE H 324 TYR 0.017 0.001 TYR F 466 ARG 0.009 0.000 ARG C 68 *********************** 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 328 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 230 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7029 (t) cc_final: 0.6454 (p) REVERT: A 178 MET cc_start: 0.3653 (OUTLIER) cc_final: 0.3221 (mtt) REVERT: A 195 ILE cc_start: 0.6539 (mm) cc_final: 0.6310 (mm) REVERT: A 247 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6195 (pt0) REVERT: A 250 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.6234 (mmm) REVERT: A 273 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6975 (mp) REVERT: A 403 CYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6961 (m) REVERT: B 50 MET cc_start: 0.7329 (ppp) cc_final: 0.7116 (ppp) REVERT: B 297 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7384 (mtp) REVERT: C 39 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7575 (ttmt) REVERT: C 73 LYS cc_start: 0.7803 (pmtt) cc_final: 0.7398 (ptmm) REVERT: C 77 ASN cc_start: 0.7791 (t0) cc_final: 0.7522 (t0) REVERT: D 219 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7642 (tpm-80) REVERT: E 95 GLU cc_start: 0.5879 (OUTLIER) cc_final: 0.5659 (mt-10) REVERT: E 103 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7717 (t0) REVERT: E 160 LYS cc_start: 0.8099 (ttpt) cc_final: 0.7739 (ptpp) REVERT: E 165 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7836 (tt) REVERT: E 220 LYS cc_start: 0.8167 (tppp) cc_final: 0.7632 (mppt) REVERT: E 314 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8515 (p0) REVERT: F 93 MET cc_start: 0.3651 (mpp) cc_final: 0.1766 (mtm) REVERT: F 119 MET cc_start: 0.3002 (ptt) cc_final: 0.2229 (ptp) REVERT: F 407 GLU cc_start: 0.6626 (mt-10) cc_final: 0.5950 (mt-10) REVERT: F 472 LYS cc_start: 0.8080 (ttmm) cc_final: 0.7787 (tttp) REVERT: G 250 LYS cc_start: 0.7450 (tttp) cc_final: 0.6959 (tmtt) REVERT: H 284 MET cc_start: 0.4222 (mmt) cc_final: 0.3507 (tpt) REVERT: H 335 ILE cc_start: 0.6717 (OUTLIER) cc_final: 0.6417 (mt) outliers start: 98 outliers final: 60 residues processed: 303 average time/residue: 1.2136 time to fit residues: 422.9549 Evaluate side-chains 301 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 228 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 353 THR 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 A residue 490 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 297 MET 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 70 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 219 ARG Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 165 ILE 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 314 ASN 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 334 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 108 ASP 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 267 VAL 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 111 ASP Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 269 ILE Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 312 GLU 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 335 ILE 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 233 optimal weight: 7.9990 chunk 213 optimal weight: 0.5980 chunk 227 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 295 ASN B 146 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN D 313 ASN E 104 ASN G 190 ASN ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21722 Z= 0.353 Angle : 0.631 12.106 29501 Z= 0.320 Chirality : 0.044 0.190 3420 Planarity : 0.004 0.059 3557 Dihedral : 14.378 161.644 3231 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 4.26 % Allowed : 27.31 % Favored : 68.43 % 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: -0.03 (0.17), residues: 2469 helix: 0.52 (0.15), residues: 1217 sheet: 0.06 (0.23), residues: 525 loop : -0.77 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 339 HIS 0.012 0.001 HIS E 18 PHE 0.019 0.002 PHE E 305 TYR 0.020 0.002 TYR D 307 ARG 0.013 0.001 ARG C 68 *********************** 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 328 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 230 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.3692 (OUTLIER) cc_final: 0.3386 (mtp) REVERT: A 247 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6193 (pt0) REVERT: A 250 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.6351 (mmm) REVERT: A 273 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7062 (mp) REVERT: A 403 CYS cc_start: 0.7392 (OUTLIER) cc_final: 0.7004 (m) REVERT: B 50 MET cc_start: 0.7403 (ppp) cc_final: 0.7188 (ppp) REVERT: B 272 ARG cc_start: 0.7888 (mmm160) cc_final: 0.7672 (mtm-85) REVERT: C 77 ASN cc_start: 0.8005 (t0) cc_final: 0.7609 (t0) REVERT: C 197 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7841 (tt) REVERT: D 219 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7682 (tpm-80) REVERT: E 160 LYS cc_start: 0.8123 (ttpt) cc_final: 0.7801 (ptpp) REVERT: E 220 LYS cc_start: 0.8243 (tppp) cc_final: 0.7676 (mppt) REVERT: F 209 VAL cc_start: 0.2819 (OUTLIER) cc_final: 0.2590 (m) REVERT: F 264 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6300 (mp) REVERT: F 407 GLU cc_start: 0.6534 (mt-10) cc_final: 0.5894 (mt-10) REVERT: F 472 LYS cc_start: 0.8074 (ttmm) cc_final: 0.7766 (tttp) REVERT: G 328 MET cc_start: 0.4590 (ttm) cc_final: 0.2829 (ppp) REVERT: H 284 MET cc_start: 0.4334 (mmt) cc_final: 0.3587 (tpt) outliers start: 98 outliers final: 53 residues processed: 304 average time/residue: 1.1750 time to fit residues: 411.4308 Evaluate side-chains 287 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 225 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 353 THR 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 A residue 467 SER Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 219 ARG Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain E residue 35 ASP 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 314 ASN 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 334 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 267 VAL 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 111 ASP Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 312 GLU Chi-restraints excluded: chain H residue 54 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 240 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 167 optimal weight: 0.9980 chunk 252 optimal weight: 4.9990 chunk 231 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 155 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 146 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 HIS G 190 ASN ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21722 Z= 0.203 Angle : 0.575 12.065 29501 Z= 0.289 Chirality : 0.041 0.223 3420 Planarity : 0.004 0.038 3557 Dihedral : 14.203 153.411 3231 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.08 % Favored : 96.88 % Rotamer: Outliers : 3.04 % Allowed : 28.88 % Favored : 68.09 % 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: 0.85 (0.15), residues: 1195 sheet: 0.06 (0.23), residues: 527 loop : -0.69 (0.24), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 42 HIS 0.006 0.001 HIS E 18 PHE 0.047 0.002 PHE H 324 TYR 0.013 0.001 TYR D 307 ARG 0.009 0.000 ARG C 68 ********************** 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 308 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 238 time to evaluate : 2.485 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 74 CYS cc_start: 0.6940 (t) cc_final: 0.6515 (p) REVERT: A 247 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6242 (pt0) REVERT: A 250 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.6436 (mmm) REVERT: A 273 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6956 (mp) REVERT: A 403 CYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6977 (m) REVERT: B 131 MET cc_start: 0.7635 (mtp) cc_final: 0.7394 (mtp) REVERT: B 272 ARG cc_start: 0.7874 (mmm160) cc_final: 0.7658 (mtm-85) REVERT: C 39 LYS cc_start: 0.7846 (mtpp) cc_final: 0.7505 (ttmm) REVERT: C 77 ASN cc_start: 0.7889 (t0) cc_final: 0.7536 (t0) REVERT: C 197 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7771 (tt) REVERT: C 207 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7142 (tpt170) REVERT: E 95 GLU cc_start: 0.6426 (tt0) cc_final: 0.6198 (mt-10) REVERT: E 160 LYS cc_start: 0.8143 (ttpt) cc_final: 0.7786 (ptpp) REVERT: E 220 LYS cc_start: 0.8189 (tppp) cc_final: 0.7640 (mppt) REVERT: E 314 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8552 (p0) REVERT: F 93 MET cc_start: 0.3442 (mpp) cc_final: 0.1513 (mtm) REVERT: F 426 GLU cc_start: 0.5164 (mp0) cc_final: 0.2832 (mm-30) REVERT: F 472 LYS cc_start: 0.8086 (ttmm) cc_final: 0.7779 (tttp) REVERT: G 328 MET cc_start: 0.4676 (ttm) cc_final: 0.2953 (ppp) REVERT: H 284 MET cc_start: 0.4345 (mmt) cc_final: 0.3561 (tpt) REVERT: H 335 ILE cc_start: 0.6589 (mm) cc_final: 0.6138 (mt) outliers start: 70 outliers final: 53 residues processed: 293 average time/residue: 1.2507 time to fit residues: 421.3231 Evaluate side-chains 289 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 229 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 353 THR 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 A residue 467 SER Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 135 SER 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 23 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR 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 311 ASN Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 88 VAL 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 314 ASN 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 334 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 437 SER Chi-restraints excluded: chain G residue 15 THR 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 111 ASP Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 270 LEU Chi-restraints excluded: chain G residue 312 GLU Chi-restraints excluded: chain H residue 54 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 213 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 201 optimal weight: 0.1980 chunk 84 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 146 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS G 20 HIS ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.202647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.145603 restraints weight = 24185.374| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.20 r_work: 0.3528 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3246 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= 0.222 Angle : 0.575 11.977 29501 Z= 0.290 Chirality : 0.041 0.224 3420 Planarity : 0.004 0.038 3557 Dihedral : 14.140 149.226 3231 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.56 % Rotamer: Outliers : 3.00 % Allowed : 28.88 % Favored : 68.13 % 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: 0.30 (0.17), residues: 2469 helix: 0.88 (0.15), residues: 1196 sheet: 0.10 (0.23), residues: 526 loop : -0.65 (0.23), residues: 747 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 0.029 0.001 PHE H 94 TYR 0.015 0.001 TYR C 52 ARG 0.009 0.000 ARG C 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7768.10 seconds wall clock time: 138 minutes 18.77 seconds (8298.77 seconds total)