Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 10 12:53:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs4_29413/07_2023/8fs4_29413_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs4_29413/07_2023/8fs4_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_29413/07_2023/8fs4_29413.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs4_29413/07_2023/8fs4_29413.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs4_29413/07_2023/8fs4_29413_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs4_29413/07_2023/8fs4_29413_updated.pdb" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 15 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: 10.41, per 1000 atoms: 0.49 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: 9.28 Conformation dependent library (CDL) restraints added in 3.0 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: 7.55 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: 8.61 Time building geometry restraints manager: 9.91 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: 12434 35.46 - 70.91: 617 70.91 - 106.37: 27 106.37 - 141.82: 1 141.82 - 177.28: 2 Dihedral angle restraints: 13081 sinusoidal: 5641 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 13078 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: 6.250 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 17.400 Check model and map are aligned: 0.290 Set scattering table: 0.210 Process input model: 61.310 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.120 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: 0.020 Load rotamer database and sin/cos tables:14.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.130 ------------------------------------------------------------------------------- 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 : 18.369 177.279 8221 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 % 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 *********************** 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 : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 54 residues processed: 303 average time/residue: 1.1252 time to fit residues: 396.1622 Evaluate side-chains 281 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 227 time to evaluate : 2.529 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 52 residues processed: 2 average time/residue: 0.9738 time to fit residues: 5.8989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 229 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 366 ASN A 411 ASN A 436 HIS C 333 ASN D 255 GLN D 340 HIS E 144 ASN E 243 ASN E 244 ASN F 8 ASN F 261 HIS G 74 ASN G 190 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 21722 Z= 0.247 Angle : 0.578 7.809 29501 Z= 0.303 Chirality : 0.043 0.203 3420 Planarity : 0.004 0.057 3557 Dihedral : 14.140 167.085 3149 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 6.30 % 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: -0.02 (0.17), residues: 2469 helix: 0.65 (0.16), residues: 1204 sheet: -0.17 (0.24), residues: 517 loop : -0.79 (0.23), residues: 748 *********************** 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 418 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 273 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 76 residues processed: 384 average time/residue: 1.0481 time to fit residues: 471.6924 Evaluate side-chains 307 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 231 time to evaluate : 2.351 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 60 residues processed: 16 average time/residue: 0.3411 time to fit residues: 11.6317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 127 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 204 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 184 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 B 146 GLN C 180 ASN C 298 HIS C 333 ASN E 336 ASN F 57 ASN F 261 HIS F 291 HIS G 190 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.094 21722 Z= 0.330 Angle : 0.605 9.798 29501 Z= 0.313 Chirality : 0.044 0.181 3420 Planarity : 0.004 0.054 3557 Dihedral : 14.261 164.203 3149 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 7.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2469 helix: 0.45 (0.15), residues: 1202 sheet: -0.19 (0.23), residues: 522 loop : -0.84 (0.23), residues: 745 *********************** 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 414 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 251 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 163 outliers final: 87 residues processed: 374 average time/residue: 1.0858 time to fit residues: 474.5508 Evaluate side-chains 319 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 232 time to evaluate : 2.429 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 67 residues processed: 20 average time/residue: 0.3948 time to fit residues: 14.7460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 227 optimal weight: 30.0000 chunk 173 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 chunk 230 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 411 ASN B 145 ASN B 146 GLN C 333 ASN D 255 GLN D 352 GLN F 261 HIS ** G 164 HIS ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 21722 Z= 0.199 Angle : 0.537 8.810 29501 Z= 0.276 Chirality : 0.041 0.147 3420 Planarity : 0.003 0.047 3557 Dihedral : 14.142 150.601 3149 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.04 % Favored : 96.92 % Rotamer Outliers : 6.21 % 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: 0.12 (0.17), residues: 2469 helix: 0.77 (0.15), residues: 1195 sheet: -0.11 (0.23), residues: 523 loop : -0.69 (0.24), residues: 751 *********************** 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 390 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 247 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 84 residues processed: 358 average time/residue: 1.1373 time to fit residues: 472.9206 Evaluate side-chains 302 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 218 time to evaluate : 2.472 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 70 residues processed: 14 average time/residue: 0.4961 time to fit residues: 12.8002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 203 optimal weight: 0.6980 chunk 138 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 182 optimal weight: 20.0000 chunk 100 optimal weight: 0.0770 chunk 208 optimal weight: 9.9990 chunk 169 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 219 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A 295 ASN B 146 GLN C 298 HIS ** G 164 HIS ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2441 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= 0.176 Angle : 0.530 11.730 29501 Z= 0.270 Chirality : 0.041 0.293 3420 Planarity : 0.003 0.047 3557 Dihedral : 14.033 137.453 3149 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.12 % Favored : 96.84 % Rotamer Outliers : 5.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 2469 helix: 0.97 (0.15), residues: 1192 sheet: -0.00 (0.23), residues: 519 loop : -0.57 (0.24), residues: 758 *********************** 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 373 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 235 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 138 outliers final: 89 residues processed: 345 average time/residue: 1.1303 time to fit residues: 455.4046 Evaluate side-chains 310 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 221 time to evaluate : 2.439 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 75 residues processed: 15 average time/residue: 0.4840 time to fit residues: 14.3230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 82 optimal weight: 4.9990 chunk 220 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 244 optimal weight: 30.0000 chunk 203 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 80 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 146 GLN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2618 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= 0.179 Angle : 0.528 8.860 29501 Z= 0.269 Chirality : 0.041 0.202 3420 Planarity : 0.003 0.039 3557 Dihedral : 13.905 127.744 3149 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.12 % Favored : 96.84 % Rotamer Outliers : 5.69 % 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: 0.48 (0.18), residues: 2469 helix: 1.06 (0.15), residues: 1192 sheet: 0.09 (0.23), residues: 517 loop : -0.54 (0.23), residues: 760 *********************** 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 371 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 240 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 82 residues processed: 354 average time/residue: 1.1550 time to fit residues: 475.5145 Evaluate side-chains 312 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 230 time to evaluate : 2.343 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 75 residues processed: 9 average time/residue: 0.4108 time to fit residues: 8.8643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 138 optimal weight: 3.9990 chunk 206 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 243 optimal weight: 30.0000 chunk 152 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 35 GLN B 146 GLN ** 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: 0.7670 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 21722 Z= 0.247 Angle : 0.562 11.282 29501 Z= 0.285 Chirality : 0.042 0.202 3420 Planarity : 0.004 0.043 3557 Dihedral : 13.904 130.456 3149 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.52 % Rotamer Outliers : 5.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.17), residues: 2469 helix: 0.97 (0.15), residues: 1193 sheet: 0.09 (0.23), residues: 513 loop : -0.56 (0.23), residues: 763 *********************** 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 367 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 238 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 129 outliers final: 87 residues processed: 345 average time/residue: 1.1173 time to fit residues: 452.5787 Evaluate side-chains 313 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 226 time to evaluate : 2.553 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 77 residues processed: 11 average time/residue: 0.4728 time to fit residues: 10.5615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 150 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 120 optimal weight: 0.0870 chunk 22 optimal weight: 4.9990 chunk 191 optimal weight: 0.2980 chunk 221 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2909 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= 0.177 Angle : 0.545 12.294 29501 Z= 0.275 Chirality : 0.041 0.229 3420 Planarity : 0.003 0.038 3557 Dihedral : 13.796 128.529 3149 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.16 % Favored : 96.80 % Rotamer Outliers : 4.82 % 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: 0.55 (0.18), residues: 2469 helix: 1.12 (0.15), residues: 1190 sheet: 0.09 (0.23), residues: 520 loop : -0.49 (0.24), residues: 759 *********************** 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 345 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 234 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 83 residues processed: 331 average time/residue: 1.1365 time to fit residues: 439.1045 Evaluate side-chains 314 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 231 time to evaluate : 2.318 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 76 residues processed: 8 average time/residue: 0.4653 time to fit residues: 8.6475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 233 optimal weight: 9.9990 chunk 213 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 205 optimal weight: 7.9990 chunk 214 optimal weight: 0.9990 chunk 226 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 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: 0.7712 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 21722 Z= 0.330 Angle : 0.614 11.664 29501 Z= 0.309 Chirality : 0.044 0.214 3420 Planarity : 0.004 0.054 3557 Dihedral : 13.922 150.907 3149 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer Outliers : 4.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2469 helix: 0.77 (0.15), residues: 1191 sheet: 0.05 (0.23), residues: 514 loop : -0.64 (0.23), residues: 764 *********************** 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 342 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 229 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 84 residues processed: 325 average time/residue: 1.2268 time to fit residues: 466.9441 Evaluate side-chains 305 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 221 time to evaluate : 2.452 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 73 residues processed: 13 average time/residue: 0.5507 time to fit residues: 12.7369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 240 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 167 optimal weight: 0.2980 chunk 252 optimal weight: 4.9990 chunk 231 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 298 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: 0.7671 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 21722 Z= 0.216 Angle : 0.576 12.064 29501 Z= 0.290 Chirality : 0.042 0.212 3420 Planarity : 0.004 0.038 3557 Dihedral : 13.882 150.659 3149 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.20 % Favored : 96.76 % Rotamer Outliers : 3.52 % 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: 0.35 (0.17), residues: 2469 helix: 0.92 (0.15), residues: 1191 sheet: 0.06 (0.23), residues: 514 loop : -0.57 (0.23), residues: 764 ********************** 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 314 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 233 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 76 residues processed: 306 average time/residue: 1.1801 time to fit residues: 418.7916 Evaluate side-chains 301 residues out of total 2303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 225 time to evaluate : 2.248 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 71 residues processed: 7 average time/residue: 0.2886 time to fit residues: 6.7335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.201367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.145189 restraints weight = 24358.682| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.25 r_work: 0.3528 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 21722 Z= 0.243 Angle : 0.581 11.426 29501 Z= 0.294 Chirality : 0.042 0.204 3420 Planarity : 0.004 0.044 3557 Dihedral : 13.865 151.493 3149 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.40 % Rotamer Outliers : 3.78 % 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: 0.87 (0.15), residues: 1191 sheet: 0.05 (0.23), residues: 515 loop : -0.59 (0.23), residues: 763 =============================================================================== Job complete usr+sys time: 7825.27 seconds wall clock time: 140 minutes 15.21 seconds (8415.21 seconds total)