Starting phenix.real_space_refine on Sat Feb 17 14:42:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ces_7464/02_2024/6ces_7464_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ces_7464/02_2024/6ces_7464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ces_7464/02_2024/6ces_7464.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ces_7464/02_2024/6ces_7464.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ces_7464/02_2024/6ces_7464_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ces_7464/02_2024/6ces_7464_neut_updated.pdb" } resolution = 4.0 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= 0.001 sd= 0.008 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 111 5.16 5 C 12147 2.51 5 N 3205 2.21 5 O 3522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N ARG 6": "NH1" <-> "NH2" Residue "N ARG 78": "NH1" <-> "NH2" Residue "N ARG 144": "NH1" <-> "NH2" Residue "N ARG 204": "NH1" <-> "NH2" Residue "N ARG 221": "NH1" <-> "NH2" Residue "N TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 279": "NH1" <-> "NH2" Residue "N ARG 324": "NH1" <-> "NH2" Residue "M PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 30": "NH1" <-> "NH2" Residue "M ARG 116": "NH1" <-> "NH2" Residue "M ARG 131": "NH1" <-> "NH2" Residue "M ARG 148": "NH1" <-> "NH2" Residue "M TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 256": "NH1" <-> "NH2" Residue "M ARG 401": "NH1" <-> "NH2" Residue "M ARG 422": "NH1" <-> "NH2" Residue "M ARG 424": "NH1" <-> "NH2" Residue "M ARG 433": "NH1" <-> "NH2" Residue "M ARG 515": "NH1" <-> "NH2" Residue "M PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 521": "NH1" <-> "NH2" Residue "M ARG 548": "NH1" <-> "NH2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D ARG 138": "NH1" <-> "NH2" Residue "D TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 347": "NH1" <-> "NH2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 763": "NH1" <-> "NH2" Residue "D TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 843": "NH1" <-> "NH2" Residue "D ARG 974": "NH1" <-> "NH2" Residue "D ARG 988": "NH1" <-> "NH2" Residue "D ARG 1087": "NH1" <-> "NH2" Residue "D ARG 1101": "NH1" <-> "NH2" Residue "D PHE 1294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1583": "NH1" <-> "NH2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "C TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 342": "NH1" <-> "NH2" Residue "C PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18988 Number of models: 1 Model: "" Number of chains: 6 Chain: "N" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2579 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 16, 'TRANS': 304} Chain breaks: 3 Chain: "M" Number of atoms: 4084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4084 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 34, 'TRANS': 484} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 7349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 7349 Classifications: {'peptide': 901} Link IDs: {'PTRANS': 44, 'TRANS': 856} Chain breaks: 10 Chain: "A" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2459 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 6, 'TRANS': 293} Chain: "C" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2485 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 8, 'TRANS': 298} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GNP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.24, per 1000 atoms: 0.54 Number of scatterers: 18988 At special positions: 0 Unit cell: (132.3, 130.95, 189, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 111 16.00 P 3 15.00 O 3522 8.00 N 3205 7.00 C 12147 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: 6.58 Conformation dependent library (CDL) restraints added in 3.4 seconds 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4514 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 18 sheets defined 30.7% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'N' and resid 40 through 46 Processing helix chain 'N' and resid 99 through 115 Processing helix chain 'N' and resid 118 through 120 No H-bonds generated for 'chain 'N' and resid 118 through 120' Processing helix chain 'N' and resid 122 through 141 removed outlier: 4.058A pdb=" N VAL N 129 " --> pdb=" O LYS N 125 " (cutoff:3.500A) Proline residue: N 130 - end of helix removed outlier: 4.119A pdb=" N ASN N 140 " --> pdb=" O LEU N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 183 No H-bonds generated for 'chain 'N' and resid 181 through 183' Processing helix chain 'N' and resid 191 through 200 Proline residue: N 198 - end of helix Processing helix chain 'N' and resid 205 through 211 removed outlier: 4.004A pdb=" N SER N 210 " --> pdb=" O ILE N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 217 through 230 Processing helix chain 'N' and resid 255 through 263 removed outlier: 3.985A pdb=" N SER N 259 " --> pdb=" O VAL N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 285 removed outlier: 5.111A pdb=" N PHE N 282 " --> pdb=" O LEU N 278 " (cutoff:3.500A) Processing helix chain 'N' and resid 352 through 358 Processing helix chain 'N' and resid 362 through 368 Processing helix chain 'M' and resid 64 through 72 Processing helix chain 'M' and resid 136 through 149 Processing helix chain 'M' and resid 161 through 172 removed outlier: 3.805A pdb=" N LEU M 171 " --> pdb=" O ALA M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 194 Processing helix chain 'M' and resid 204 through 212 Processing helix chain 'M' and resid 246 through 251 Processing helix chain 'M' and resid 258 through 269 Processing helix chain 'M' and resid 293 through 304 Processing helix chain 'M' and resid 337 through 345 Processing helix chain 'M' and resid 355 through 358 No H-bonds generated for 'chain 'M' and resid 355 through 358' Processing helix chain 'M' and resid 364 through 378 Proline residue: M 371 - end of helix Processing helix chain 'M' and resid 382 through 386 Processing helix chain 'M' and resid 391 through 393 No H-bonds generated for 'chain 'M' and resid 391 through 393' Processing helix chain 'M' and resid 395 through 401 Processing helix chain 'M' and resid 477 through 485 Processing helix chain 'M' and resid 493 through 500 Processing helix chain 'M' and resid 515 through 519 Processing helix chain 'M' and resid 524 through 531 Processing helix chain 'M' and resid 539 through 545 removed outlier: 4.137A pdb=" N PHE M 544 " --> pdb=" O LEU M 540 " (cutoff:3.500A) Processing helix chain 'M' and resid 559 through 566 Processing helix chain 'D' and resid 71 through 75 Processing helix chain 'D' and resid 111 through 120 Processing helix chain 'D' and resid 191 through 209 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 269 through 286 Proline residue: D 282 - end of helix Processing helix chain 'D' and resid 306 through 319 removed outlier: 4.758A pdb=" N LYS D 319 " --> pdb=" O ASN D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 357 Processing helix chain 'D' and resid 744 through 748 removed outlier: 4.141A pdb=" N THR D 748 " --> pdb=" O LYS D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 805 Processing helix chain 'D' and resid 976 through 990 removed outlier: 4.325A pdb=" N VAL D 990 " --> pdb=" O PHE D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 1090 through 1101 Proline residue: D1100 - end of helix Processing helix chain 'D' and resid 1180 through 1185 Processing helix chain 'D' and resid 1207 through 1217 Processing helix chain 'D' and resid 1223 through 1231 Processing helix chain 'D' and resid 1304 through 1311 Proline residue: D1309 - end of helix Processing helix chain 'D' and resid 1395 through 1410 Processing helix chain 'D' and resid 1465 through 1483 Processing helix chain 'D' and resid 1567 through 1580 Processing helix chain 'D' and resid 1586 through 1595 Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 35 through 38 removed outlier: 3.814A pdb=" N ARG A 38 " --> pdb=" O ASP A 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 35 through 38' Processing helix chain 'A' and resid 67 through 74 Processing helix chain 'A' and resid 78 through 81 No H-bonds generated for 'chain 'A' and resid 78 through 81' Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 134 through 151 Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 185 through 197 Processing helix chain 'A' and resid 226 through 245 removed outlier: 4.103A pdb=" N LYS A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 297 removed outlier: 4.144A pdb=" N HIS A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 90 through 93 removed outlier: 3.892A pdb=" N LEU C 93 " --> pdb=" O THR C 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 93' Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 127 through 133 removed outlier: 3.881A pdb=" N MET C 132 " --> pdb=" O PHE C 128 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 167 removed outlier: 4.993A pdb=" N HIS C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE C 159 " --> pdb=" O THR C 155 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA C 164 " --> pdb=" O THR C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 198 removed outlier: 3.715A pdb=" N ILE C 195 " --> pdb=" O THR C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 234 Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 281 through 297 Processing helix chain 'C' and resid 353 through 366 Processing sheet with id= A, first strand: chain 'N' and resid 22 through 27 removed outlier: 3.810A pdb=" N GLU N 8 " --> pdb=" O VAL N 88 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL N 88 " --> pdb=" O GLU N 8 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ILE N 10 " --> pdb=" O GLY N 86 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLY N 86 " --> pdb=" O ILE N 10 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE N 12 " --> pdb=" O ASN N 84 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN N 84 " --> pdb=" O PHE N 12 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLU N 14 " --> pdb=" O LEU N 82 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU N 82 " --> pdb=" O GLU N 14 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 144 through 148 Processing sheet with id= C, first strand: chain 'N' and resid 174 through 177 Processing sheet with id= D, first strand: chain 'M' and resid 9 through 11 removed outlier: 4.064A pdb=" N VAL M 126 " --> pdb=" O HIS M 96 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS M 96 " --> pdb=" O VAL M 126 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE M 128 " --> pdb=" O VAL M 94 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL M 94 " --> pdb=" O PHE M 128 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU M 130 " --> pdb=" O ARG M 92 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'M' and resid 47 through 49 Processing sheet with id= F, first strand: chain 'M' and resid 429 through 432 Processing sheet with id= G, first strand: chain 'D' and resid 39 through 42 Processing sheet with id= H, first strand: chain 'D' and resid 161 through 166 Processing sheet with id= I, first strand: chain 'D' and resid 123 through 127 Processing sheet with id= J, first strand: chain 'D' and resid 405 through 407 removed outlier: 9.184A pdb=" N SER D 406 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP D 365 " --> pdb=" O SER D 406 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL D 364 " --> pdb=" O GLN D 331 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N SER D 333 " --> pdb=" O VAL D 364 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU D 366 " --> pdb=" O SER D 333 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL D 335 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N MET D 170 " --> pdb=" O MET D 332 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL D 334 " --> pdb=" O MET D 170 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TYR D 172 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE D 336 " --> pdb=" O TYR D 172 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE D 174 " --> pdb=" O ILE D 336 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLU D 215 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE D 173 " --> pdb=" O GLU D 215 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR D 217 " --> pdb=" O ILE D 173 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE D 175 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL D 219 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS D 247 " --> pdb=" O ILE D 242 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 342 through 345 removed outlier: 6.556A pdb=" N LEU D 379 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL D 345 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LYS D 381 " --> pdb=" O VAL D 345 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 770 through 774 removed outlier: 6.689A pdb=" N TRP D 853 " --> pdb=" O THR D 771 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLY D 773 " --> pdb=" O TRP D 853 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N SER D 855 " --> pdb=" O GLY D 773 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR D 852 " --> pdb=" O LYS D 868 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 1415 through 1418 removed outlier: 3.720A pdb=" N LEU D1415 " --> pdb=" O ALA D1300 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 1439 through 1441 removed outlier: 3.607A pdb=" N ILE D1441 " --> pdb=" O TYR D1546 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL D1509 " --> pdb=" O HIS D1504 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 157 through 161 removed outlier: 6.979A pdb=" N ILE A 122 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N PHE A 160 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS A 124 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLY A 14 " --> pdb=" O CYS A 63 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 251 through 256 removed outlier: 3.990A pdb=" N PHE A 259 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLU A 207 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL A 213 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 141 through 144 removed outlier: 8.711A pdb=" N TYR C 142 " --> pdb=" O ASN C 172 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLU C 174 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE C 144 " --> pdb=" O GLU C 174 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE C 176 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 259 through 262 removed outlier: 4.185A pdb=" N TYR C 327 " --> pdb=" O CYS C 339 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.35 Time building geometry restraints manager: 7.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4649 1.33 - 1.45: 4089 1.45 - 1.58: 10497 1.58 - 1.70: 6 1.70 - 1.82: 172 Bond restraints: 19413 Sorted by residual: bond pdb=" O2B GNP A 500 " pdb=" PB GNP A 500 " ideal model delta sigma weight residual 1.505 1.604 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C4 GNP A 500 " pdb=" C5 GNP A 500 " ideal model delta sigma weight residual 1.382 1.464 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" O1G GNP A 500 " pdb=" PG GNP A 500 " ideal model delta sigma weight residual 1.531 1.608 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" O3G GNP A 500 " pdb=" PG GNP A 500 " ideal model delta sigma weight residual 1.532 1.609 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C ASP C 125 " pdb=" N PRO C 126 " ideal model delta sigma weight residual 1.336 1.381 -0.046 1.23e-02 6.61e+03 1.39e+01 ... (remaining 19408 not shown) Histogram of bond angle deviations from ideal: 96.62 - 104.51: 357 104.51 - 112.40: 9283 112.40 - 120.29: 8899 120.29 - 128.18: 7547 128.18 - 136.07: 207 Bond angle restraints: 26293 Sorted by residual: angle pdb=" C VAL C 277 " pdb=" N ASP C 278 " pdb=" CA ASP C 278 " ideal model delta sigma weight residual 121.54 132.13 -10.59 1.91e+00 2.74e-01 3.07e+01 angle pdb=" C PRO M 502 " pdb=" N ALA M 503 " pdb=" CA ALA M 503 " ideal model delta sigma weight residual 121.54 131.72 -10.18 1.91e+00 2.74e-01 2.84e+01 angle pdb=" C LYS M 87 " pdb=" N ILE M 88 " pdb=" CA ILE M 88 " ideal model delta sigma weight residual 122.27 127.87 -5.60 1.07e+00 8.73e-01 2.74e+01 angle pdb=" C PRO D1495 " pdb=" N ALA D1496 " pdb=" CA ALA D1496 " ideal model delta sigma weight residual 121.54 131.46 -9.92 1.91e+00 2.74e-01 2.70e+01 angle pdb=" C TYR N 245 " pdb=" N CYS N 246 " pdb=" CA CYS N 246 " ideal model delta sigma weight residual 120.06 126.14 -6.08 1.19e+00 7.06e-01 2.61e+01 ... (remaining 26288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 10811 17.39 - 34.78: 765 34.78 - 52.16: 140 52.16 - 69.55: 5 69.55 - 86.94: 7 Dihedral angle restraints: 11728 sinusoidal: 4803 harmonic: 6925 Sorted by residual: dihedral pdb=" CA ARG D1583 " pdb=" C ARG D1583 " pdb=" N ASP D1584 " pdb=" CA ASP D1584 " ideal model delta harmonic sigma weight residual -180.00 -126.01 -53.99 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" CA ASN M 379 " pdb=" C ASN M 379 " pdb=" N PRO M 380 " pdb=" CA PRO M 380 " ideal model delta harmonic sigma weight residual 180.00 133.77 46.23 0 5.00e+00 4.00e-02 8.55e+01 dihedral pdb=" CA GLU D 288 " pdb=" C GLU D 288 " pdb=" N GLN D 289 " pdb=" CA GLN D 289 " ideal model delta harmonic sigma weight residual -180.00 -136.20 -43.80 0 5.00e+00 4.00e-02 7.68e+01 ... (remaining 11725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2451 0.086 - 0.171: 418 0.171 - 0.257: 59 0.257 - 0.342: 5 0.342 - 0.428: 4 Chirality restraints: 2937 Sorted by residual: chirality pdb=" CB ILE C 237 " pdb=" CA ILE C 237 " pdb=" CG1 ILE C 237 " pdb=" CG2 ILE C 237 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CB ILE M 11 " pdb=" CA ILE M 11 " pdb=" CG1 ILE M 11 " pdb=" CG2 ILE M 11 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CA THR M 441 " pdb=" N THR M 441 " pdb=" C THR M 441 " pdb=" CB THR M 441 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.35 2.00e-01 2.50e+01 3.04e+00 ... (remaining 2934 not shown) Planarity restraints: 3363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 298 " -0.031 2.00e-02 2.50e+03 6.05e-02 3.66e+01 pdb=" C GLU A 298 " 0.105 2.00e-02 2.50e+03 pdb=" O GLU A 298 " -0.039 2.00e-02 2.50e+03 pdb=" N LYS A 299 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 173 " 0.038 2.00e-02 2.50e+03 2.58e-02 1.67e+01 pdb=" CG TRP A 173 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP A 173 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 173 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 173 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 173 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 173 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 173 " 0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 173 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 173 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN M 379 " 0.066 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO M 380 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO M 380 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO M 380 " 0.055 5.00e-02 4.00e+02 ... (remaining 3360 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3110 2.77 - 3.30: 17843 3.30 - 3.83: 29923 3.83 - 4.37: 33193 4.37 - 4.90: 55534 Nonbonded interactions: 139603 Sorted by model distance: nonbonded pdb=" O THR N 58 " pdb=" O LYS M 87 " model vdw 2.231 3.040 nonbonded pdb=" O VAL M 67 " pdb=" OG1 THR M 71 " model vdw 2.267 2.440 nonbonded pdb=" O ALA A 172 " pdb=" OG SER A 175 " model vdw 2.268 2.440 nonbonded pdb=" O ILE N 354 " pdb=" OG1 THR N 358 " model vdw 2.277 2.440 nonbonded pdb=" O ASP A 44 " pdb=" OH TYR A 73 " model vdw 2.279 2.440 ... (remaining 139598 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 group one per residue 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 2.690 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 48.550 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 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 : 0.007 0.099 19413 Z= 0.465 Angle : 1.322 15.065 26293 Z= 0.694 Chirality : 0.067 0.428 2937 Planarity : 0.010 0.100 3363 Dihedral : 12.250 86.941 7214 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.43 % Allowed : 16.77 % Favored : 82.80 % Rotamer: Outliers : 0.99 % Allowed : 6.24 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.67 % Twisted General : 0.72 % 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: -5.29 (0.13), residues: 2302 helix: -2.85 (0.13), residues: 750 sheet: -2.32 (0.23), residues: 404 loop : -4.57 (0.13), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.004 TRP A 173 HIS 0.015 0.003 HIS D1186 PHE 0.036 0.004 PHE C 226 TYR 0.031 0.004 TYR D 226 ARG 0.015 0.001 ARG D 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 306 time to evaluate : 2.362 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: N 269 THR cc_start: 0.6837 (m) cc_final: 0.6543 (p) REVERT: M 250 ARG cc_start: 0.5318 (tmt90) cc_final: 0.5036 (ttp80) REVERT: M 262 LEU cc_start: 0.8210 (mt) cc_final: 0.7534 (mm) REVERT: M 404 ILE cc_start: 0.7430 (mm) cc_final: 0.6864 (mm) REVERT: M 530 MET cc_start: 0.7151 (mmm) cc_final: 0.6948 (mmt) REVERT: D 59 LYS cc_start: 0.6301 (mtpp) cc_final: 0.5880 (mmpt) REVERT: D 853 TRP cc_start: 0.8470 (p-90) cc_final: 0.8239 (p-90) REVERT: D 868 LYS cc_start: 0.8356 (ttmt) cc_final: 0.8022 (mmtm) REVERT: D 1253 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7826 (m-10) REVERT: A 3 ASN cc_start: 0.7359 (t0) cc_final: 0.6810 (m-40) REVERT: A 90 TYR cc_start: 0.8382 (t80) cc_final: 0.8178 (t80) REVERT: A 252 MET cc_start: 0.6490 (OUTLIER) cc_final: 0.6274 (ppp) REVERT: A 266 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.7012 (m-10) REVERT: C 67 MET cc_start: 0.3730 (mtt) cc_final: 0.3371 (ppp) outliers start: 21 outliers final: 4 residues processed: 324 average time/residue: 0.3554 time to fit residues: 167.7463 Evaluate side-chains 174 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 167 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain C residue 175 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 196 optimal weight: 0.7980 chunk 176 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 94 optimal weight: 0.4980 chunk 182 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 211 optimal weight: 9.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 321 ASN M 50 ASN M 144 ASN M 192 HIS ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 493 HIS M 524 HIS D 45 ASN D 176 GLN D 197 ASN D 261 ASN ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN D 315 ASN D 383 HIS D 384 ASN ** D 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 981 GLN D 994 ASN ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1389 HIS D1478 HIS D1551 ASN ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 186 GLN A 258 ASN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 ASN C 111 ASN ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN C 364 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19413 Z= 0.258 Angle : 0.815 9.994 26293 Z= 0.423 Chirality : 0.047 0.258 2937 Planarity : 0.007 0.080 3363 Dihedral : 8.653 87.362 2579 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 15.29 % Favored : 84.62 % Rotamer: Outliers : 2.88 % Allowed : 10.40 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.80 % Twisted General : 0.36 % 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: -4.31 (0.15), residues: 2302 helix: -1.38 (0.17), residues: 751 sheet: -2.14 (0.24), residues: 406 loop : -4.33 (0.14), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D1405 HIS 0.005 0.001 HIS D1375 PHE 0.029 0.002 PHE D1289 TYR 0.022 0.002 TYR C 165 ARG 0.008 0.001 ARG N 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 183 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 112 LEU cc_start: 0.8929 (mt) cc_final: 0.8678 (mt) REVERT: N 261 GLN cc_start: 0.8026 (mp-120) cc_final: 0.7690 (mp-120) REVERT: M 80 CYS cc_start: 0.7827 (t) cc_final: 0.6662 (t) REVERT: M 127 VAL cc_start: 0.7440 (t) cc_final: 0.7151 (p) REVERT: M 250 ARG cc_start: 0.5672 (tmt90) cc_final: 0.5229 (ttp80) REVERT: M 393 MET cc_start: 0.8754 (ppp) cc_final: 0.8278 (ppp) REVERT: M 397 MET cc_start: 0.8255 (ttp) cc_final: 0.8041 (ptm) REVERT: M 512 MET cc_start: 0.7597 (mmt) cc_final: 0.7335 (mmt) REVERT: D 59 LYS cc_start: 0.6376 (mtpp) cc_final: 0.5880 (mmpt) REVERT: D 236 GLU cc_start: 0.6998 (tt0) cc_final: 0.6748 (tt0) REVERT: D 853 TRP cc_start: 0.8533 (p-90) cc_final: 0.8258 (p-90) REVERT: D 868 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7716 (tppt) REVERT: D 995 ARG cc_start: 0.6173 (ttt180) cc_final: 0.5579 (mtp180) REVERT: D 1095 GLU cc_start: 0.8479 (pp20) cc_final: 0.8171 (tm-30) REVERT: A 23 MET cc_start: 0.7719 (tmm) cc_final: 0.7468 (tmm) REVERT: A 252 MET cc_start: 0.6259 (OUTLIER) cc_final: 0.6044 (ppp) REVERT: A 271 TYR cc_start: 0.7142 (m-80) cc_final: 0.6329 (m-80) REVERT: A 276 MET cc_start: 0.8412 (tpp) cc_final: 0.7742 (tpp) REVERT: C 67 MET cc_start: 0.3314 (mtt) cc_final: 0.2941 (ppp) REVERT: C 315 MET cc_start: 0.7658 (ppp) cc_final: 0.7421 (ppp) outliers start: 61 outliers final: 31 residues processed: 234 average time/residue: 0.3008 time to fit residues: 110.3611 Evaluate side-chains 190 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 158 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 118 PHE Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 345 TYR Chi-restraints excluded: chain M residue 439 LEU Chi-restraints excluded: chain M residue 482 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 815 VAL Chi-restraints excluded: chain D residue 979 GLU Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1375 HIS Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 357 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 117 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 58 optimal weight: 0.0970 chunk 211 optimal weight: 10.0000 chunk 228 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 210 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 overall best weight: 3.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 156 HIS ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 ASN D 797 GLN ** D 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 19413 Z= 0.387 Angle : 0.887 10.406 26293 Z= 0.460 Chirality : 0.050 0.248 2937 Planarity : 0.007 0.079 3363 Dihedral : 8.703 87.383 2579 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 17.33 % Favored : 82.58 % Rotamer: Outliers : 4.11 % Allowed : 13.47 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.80 % Twisted General : 0.32 % 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: -4.02 (0.16), residues: 2302 helix: -0.91 (0.18), residues: 758 sheet: -2.21 (0.23), residues: 411 loop : -4.27 (0.15), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP D1405 HIS 0.008 0.002 HIS N 205 PHE 0.027 0.003 PHE D 760 TYR 0.020 0.002 TYR D 82 ARG 0.008 0.001 ARG D 988 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 161 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 319 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7142 (mtm) REVERT: M 73 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7761 (pp) REVERT: M 79 MET cc_start: 0.6043 (ppp) cc_final: 0.4539 (ppp) REVERT: M 250 ARG cc_start: 0.5548 (tmt90) cc_final: 0.5041 (ttp80) REVERT: M 480 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: D 59 LYS cc_start: 0.6529 (mtpp) cc_final: 0.6028 (mmpt) REVERT: D 181 MET cc_start: 0.9501 (mmt) cc_final: 0.9282 (tpp) REVERT: D 868 LYS cc_start: 0.8281 (ttmt) cc_final: 0.7866 (tppt) REVERT: D 979 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8332 (pt0) REVERT: D 1095 GLU cc_start: 0.8313 (pp20) cc_final: 0.8038 (tm-30) REVERT: D 1253 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.7926 (m-10) REVERT: D 1465 TYR cc_start: 0.4784 (OUTLIER) cc_final: 0.3766 (t80) REVERT: D 1548 TRP cc_start: 0.9111 (OUTLIER) cc_final: 0.7288 (t-100) REVERT: D 1550 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.7631 (m-80) REVERT: A 189 MET cc_start: 0.6859 (tmm) cc_final: 0.6447 (tmm) REVERT: A 252 MET cc_start: 0.5665 (OUTLIER) cc_final: 0.5273 (ppp) REVERT: A 276 MET cc_start: 0.8329 (tpp) cc_final: 0.7938 (tpp) outliers start: 87 outliers final: 44 residues processed: 237 average time/residue: 0.2758 time to fit residues: 104.0968 Evaluate side-chains 198 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 145 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 118 PHE Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 319 MET Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 345 TYR Chi-restraints excluded: chain M residue 359 HIS Chi-restraints excluded: chain M residue 395 VAL Chi-restraints excluded: chain M residue 439 LEU Chi-restraints excluded: chain M residue 480 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 357 MET Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 872 VAL Chi-restraints excluded: chain D residue 979 GLU Chi-restraints excluded: chain D residue 989 PHE Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1364 THR Chi-restraints excluded: chain D residue 1375 HIS Chi-restraints excluded: chain D residue 1465 TYR Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1548 TRP Chi-restraints excluded: chain D residue 1550 TYR Chi-restraints excluded: chain D residue 1584 ASP Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 357 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 209 optimal weight: 1.9990 chunk 159 optimal weight: 0.0970 chunk 110 optimal weight: 0.8980 chunk 23 optimal weight: 40.0000 chunk 101 optimal weight: 0.8980 chunk 142 optimal weight: 0.0030 chunk 212 optimal weight: 7.9990 chunk 225 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 201 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 379 ASN D 355 GLN ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1406 HIS A 49 HIS A 59 ASN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 196 HIS C 200 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19413 Z= 0.172 Angle : 0.735 11.096 26293 Z= 0.373 Chirality : 0.045 0.220 2937 Planarity : 0.006 0.077 3363 Dihedral : 7.703 87.412 2579 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.21 % Favored : 86.75 % Rotamer: Outliers : 3.36 % Allowed : 15.26 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.80 % Twisted General : 0.32 % 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: -3.49 (0.16), residues: 2302 helix: -0.32 (0.19), residues: 766 sheet: -1.92 (0.24), residues: 395 loop : -4.08 (0.15), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D1405 HIS 0.005 0.001 HIS M 315 PHE 0.021 0.002 PHE D1311 TYR 0.020 0.001 TYR M 208 ARG 0.005 0.000 ARG C 348 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 198 time to evaluate : 2.059 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: N 112 LEU cc_start: 0.8729 (mt) cc_final: 0.8480 (mt) REVERT: N 261 GLN cc_start: 0.8172 (mp-120) cc_final: 0.7802 (mp-120) REVERT: M 73 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7724 (pp) REVERT: M 127 VAL cc_start: 0.7438 (t) cc_final: 0.7180 (p) REVERT: M 250 ARG cc_start: 0.5365 (tmt90) cc_final: 0.4973 (ttp80) REVERT: M 439 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7461 (tt) REVERT: D 59 LYS cc_start: 0.6133 (mtpp) cc_final: 0.5696 (mmpt) REVERT: D 312 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8193 (tt) REVERT: D 868 LYS cc_start: 0.8240 (ttmt) cc_final: 0.7800 (tppt) REVERT: D 995 ARG cc_start: 0.6333 (ttt180) cc_final: 0.5549 (mtp180) REVERT: D 1095 GLU cc_start: 0.8296 (pp20) cc_final: 0.8007 (tm-30) REVERT: D 1405 TRP cc_start: 0.8672 (p90) cc_final: 0.8335 (p90) REVERT: D 1465 TYR cc_start: 0.4546 (OUTLIER) cc_final: 0.3551 (t80) REVERT: D 1573 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8850 (tt) REVERT: A 189 MET cc_start: 0.6818 (tmm) cc_final: 0.6481 (tmm) REVERT: A 252 MET cc_start: 0.6319 (OUTLIER) cc_final: 0.6093 (ppp) REVERT: A 276 MET cc_start: 0.8156 (tpp) cc_final: 0.7933 (tpp) REVERT: C 67 MET cc_start: 0.2786 (mmm) cc_final: 0.1324 (tmm) REVERT: C 113 GLN cc_start: 0.6726 (mp10) cc_final: 0.6490 (mp10) REVERT: C 269 TYR cc_start: 0.2834 (m-80) cc_final: 0.2472 (m-80) outliers start: 71 outliers final: 32 residues processed: 255 average time/residue: 0.2886 time to fit residues: 115.0569 Evaluate side-chains 204 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 118 PHE Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 345 TYR Chi-restraints excluded: chain M residue 395 VAL Chi-restraints excluded: chain M residue 439 LEU Chi-restraints excluded: chain M residue 480 GLN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 870 ILE Chi-restraints excluded: chain D residue 989 PHE Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1364 THR Chi-restraints excluded: chain D residue 1465 TYR Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1573 LEU Chi-restraints excluded: chain D residue 1584 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 357 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 187 optimal weight: 10.0000 chunk 127 optimal weight: 0.0870 chunk 3 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 202 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 205 HIS ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 809 GLN ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19413 Z= 0.240 Angle : 0.766 13.926 26293 Z= 0.385 Chirality : 0.046 0.237 2937 Planarity : 0.006 0.110 3363 Dihedral : 7.640 87.876 2575 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 15.16 % Favored : 84.80 % Rotamer: Outliers : 3.40 % Allowed : 17.30 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.27 % 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: -3.34 (0.17), residues: 2302 helix: -0.10 (0.20), residues: 767 sheet: -1.91 (0.24), residues: 411 loop : -4.05 (0.15), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D1405 HIS 0.008 0.001 HIS M 96 PHE 0.023 0.002 PHE D1311 TYR 0.016 0.002 TYR D 770 ARG 0.004 0.000 ARG D 988 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 171 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 112 LEU cc_start: 0.8767 (mt) cc_final: 0.8558 (mt) REVERT: N 360 MET cc_start: 0.8082 (mpp) cc_final: 0.7851 (mpp) REVERT: M 127 VAL cc_start: 0.7403 (t) cc_final: 0.7179 (p) REVERT: M 250 ARG cc_start: 0.5418 (tmt90) cc_final: 0.4954 (ttp80) REVERT: M 439 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7573 (tt) REVERT: D 59 LYS cc_start: 0.6561 (mtpp) cc_final: 0.6013 (mmpt) REVERT: D 868 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7885 (tppt) REVERT: D 1095 GLU cc_start: 0.8420 (pp20) cc_final: 0.8052 (tm-30) REVERT: D 1253 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7876 (m-10) REVERT: D 1405 TRP cc_start: 0.8621 (p90) cc_final: 0.8189 (p90) REVERT: D 1465 TYR cc_start: 0.4562 (OUTLIER) cc_final: 0.3565 (t80) REVERT: D 1548 TRP cc_start: 0.9065 (OUTLIER) cc_final: 0.7159 (t-100) REVERT: D 1573 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8795 (tt) REVERT: A 189 MET cc_start: 0.6836 (tmm) cc_final: 0.6366 (tmm) REVERT: A 266 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6397 (m-10) REVERT: C 67 MET cc_start: 0.2930 (mmm) cc_final: 0.1616 (tmm) REVERT: C 269 TYR cc_start: 0.2518 (m-80) cc_final: 0.1960 (m-80) outliers start: 72 outliers final: 37 residues processed: 227 average time/residue: 0.2813 time to fit residues: 102.0128 Evaluate side-chains 204 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 161 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 52 ASN Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 118 PHE Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 345 TYR Chi-restraints excluded: chain M residue 395 VAL Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 439 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1364 THR Chi-restraints excluded: chain D residue 1414 PHE Chi-restraints excluded: chain D residue 1465 TYR Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1548 TRP Chi-restraints excluded: chain D residue 1573 LEU Chi-restraints excluded: chain D residue 1584 ASP Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 357 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 75 optimal weight: 9.9990 chunk 202 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 55 optimal weight: 0.0060 chunk 225 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19413 Z= 0.237 Angle : 0.762 11.679 26293 Z= 0.384 Chirality : 0.046 0.234 2937 Planarity : 0.006 0.115 3363 Dihedral : 7.553 88.117 2572 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.99 % Favored : 84.93 % Rotamer: Outliers : 3.40 % Allowed : 18.05 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.32 % 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: -3.24 (0.17), residues: 2302 helix: -0.04 (0.19), residues: 771 sheet: -1.81 (0.25), residues: 398 loop : -3.99 (0.15), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 173 HIS 0.005 0.001 HIS C 178 PHE 0.019 0.002 PHE D 760 TYR 0.016 0.002 TYR M 208 ARG 0.004 0.000 ARG D 988 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 167 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 112 LEU cc_start: 0.8761 (mt) cc_final: 0.8534 (mt) REVERT: M 127 VAL cc_start: 0.7602 (t) cc_final: 0.7339 (p) REVERT: M 439 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7557 (tt) REVERT: M 480 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: D 59 LYS cc_start: 0.6230 (mtpp) cc_final: 0.5861 (mmpt) REVERT: D 830 LEU cc_start: 0.7057 (pp) cc_final: 0.6780 (mp) REVERT: D 868 LYS cc_start: 0.8306 (ttmt) cc_final: 0.7923 (tppt) REVERT: D 995 ARG cc_start: 0.6597 (ttt180) cc_final: 0.5489 (mtp180) REVERT: D 1095 GLU cc_start: 0.8332 (pp20) cc_final: 0.8095 (tm-30) REVERT: D 1253 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7861 (m-10) REVERT: D 1405 TRP cc_start: 0.8632 (p90) cc_final: 0.8250 (p90) REVERT: D 1465 TYR cc_start: 0.4677 (OUTLIER) cc_final: 0.3739 (t80) REVERT: D 1548 TRP cc_start: 0.9047 (OUTLIER) cc_final: 0.7279 (t-100) REVERT: D 1573 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8774 (tt) REVERT: A 189 MET cc_start: 0.6851 (tmm) cc_final: 0.6380 (tmm) REVERT: A 223 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7186 (mtt-85) REVERT: A 266 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6399 (m-10) REVERT: A 271 TYR cc_start: 0.7106 (m-80) cc_final: 0.6451 (m-80) REVERT: A 276 MET cc_start: 0.7838 (tpp) cc_final: 0.7467 (tpp) REVERT: C 113 GLN cc_start: 0.6511 (mp10) cc_final: 0.6264 (mp10) REVERT: C 269 TYR cc_start: 0.2551 (m-80) cc_final: 0.2028 (m-80) outliers start: 72 outliers final: 45 residues processed: 223 average time/residue: 0.2929 time to fit residues: 103.6998 Evaluate side-chains 214 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 161 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 52 ASN Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 118 PHE Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 395 VAL Chi-restraints excluded: chain M residue 439 LEU Chi-restraints excluded: chain M residue 480 GLN Chi-restraints excluded: chain M residue 550 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 815 VAL Chi-restraints excluded: chain D residue 989 PHE Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1364 THR Chi-restraints excluded: chain D residue 1408 LYS Chi-restraints excluded: chain D residue 1414 PHE Chi-restraints excluded: chain D residue 1419 VAL Chi-restraints excluded: chain D residue 1465 TYR Chi-restraints excluded: chain D residue 1469 MET Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1543 ARG Chi-restraints excluded: chain D residue 1548 TRP Chi-restraints excluded: chain D residue 1573 LEU Chi-restraints excluded: chain D residue 1584 ASP Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 357 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 217 optimal weight: 0.0270 chunk 25 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.1240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 371 ASN M 300 GLN ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN ** D 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19413 Z= 0.185 Angle : 0.731 10.993 26293 Z= 0.364 Chirality : 0.045 0.226 2937 Planarity : 0.006 0.104 3363 Dihedral : 7.271 88.188 2572 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.38 % Favored : 85.58 % Rotamer: Outliers : 3.45 % Allowed : 18.19 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.27 % 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: -3.09 (0.17), residues: 2302 helix: 0.07 (0.19), residues: 774 sheet: -1.75 (0.24), residues: 398 loop : -3.89 (0.16), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 173 HIS 0.006 0.001 HIS A 49 PHE 0.018 0.001 PHE D1289 TYR 0.018 0.001 TYR M 208 ARG 0.003 0.000 ARG N 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 180 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 73 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.7185 (t-90) REVERT: N 112 LEU cc_start: 0.8717 (mt) cc_final: 0.8513 (mt) REVERT: N 261 GLN cc_start: 0.8107 (mp-120) cc_final: 0.7702 (mp-120) REVERT: N 371 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7619 (m-40) REVERT: M 127 VAL cc_start: 0.7509 (t) cc_final: 0.7258 (p) REVERT: M 439 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7428 (tt) REVERT: M 480 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: M 530 MET cc_start: 0.6830 (mmt) cc_final: 0.6510 (mtt) REVERT: D 59 LYS cc_start: 0.6333 (mtpp) cc_final: 0.6039 (mmpt) REVERT: D 303 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6835 (mp10) REVERT: D 830 LEU cc_start: 0.6983 (pp) cc_final: 0.6552 (mp) REVERT: D 868 LYS cc_start: 0.8342 (ttmt) cc_final: 0.7950 (tppt) REVERT: D 995 ARG cc_start: 0.6508 (ttt180) cc_final: 0.5580 (mtp180) REVERT: D 1095 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: D 1253 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7831 (m-10) REVERT: D 1405 TRP cc_start: 0.8556 (p90) cc_final: 0.8338 (p90) REVERT: D 1465 TYR cc_start: 0.4471 (OUTLIER) cc_final: 0.3821 (t80) REVERT: D 1548 TRP cc_start: 0.9025 (OUTLIER) cc_final: 0.7122 (t-100) REVERT: D 1573 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8879 (tt) REVERT: A 189 MET cc_start: 0.6862 (tmm) cc_final: 0.6391 (tmm) REVERT: A 252 MET cc_start: 0.6290 (ppp) cc_final: 0.6028 (ppp) REVERT: A 266 PHE cc_start: 0.7146 (OUTLIER) cc_final: 0.6407 (m-10) REVERT: C 67 MET cc_start: 0.2256 (mmt) cc_final: 0.0879 (tmm) REVERT: C 269 TYR cc_start: 0.2968 (m-80) cc_final: 0.2656 (m-80) REVERT: C 359 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7897 (p90) outliers start: 73 outliers final: 44 residues processed: 243 average time/residue: 0.2849 time to fit residues: 109.9487 Evaluate side-chains 220 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 164 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 52 ASN Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 73 HIS Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain N residue 371 ASN Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 395 VAL Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 439 LEU Chi-restraints excluded: chain M residue 480 GLN Chi-restraints excluded: chain M residue 550 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 303 GLN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 815 VAL Chi-restraints excluded: chain D residue 989 PHE Chi-restraints excluded: chain D residue 1095 GLU Chi-restraints excluded: chain D residue 1212 HIS Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1364 THR Chi-restraints excluded: chain D residue 1414 PHE Chi-restraints excluded: chain D residue 1419 VAL Chi-restraints excluded: chain D residue 1465 TYR Chi-restraints excluded: chain D residue 1469 MET Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1543 ARG Chi-restraints excluded: chain D residue 1548 TRP Chi-restraints excluded: chain D residue 1573 LEU Chi-restraints excluded: chain D residue 1584 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 359 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 138 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 153 optimal weight: 0.3980 chunk 111 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 176 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 339 ASN ** D 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19413 Z= 0.174 Angle : 0.730 10.549 26293 Z= 0.363 Chirality : 0.044 0.220 2937 Planarity : 0.006 0.119 3363 Dihedral : 7.092 88.043 2572 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.90 % Favored : 86.06 % Rotamer: Outliers : 2.98 % Allowed : 19.28 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.23 % 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: -2.97 (0.17), residues: 2302 helix: 0.14 (0.19), residues: 775 sheet: -1.67 (0.25), residues: 396 loop : -3.80 (0.16), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 173 HIS 0.007 0.001 HIS A 49 PHE 0.018 0.001 PHE D1289 TYR 0.018 0.001 TYR M 208 ARG 0.005 0.000 ARG C 348 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 173 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 73 HIS cc_start: 0.7954 (OUTLIER) cc_final: 0.7038 (t-90) REVERT: N 132 MET cc_start: 0.8957 (mtm) cc_final: 0.8614 (mtm) REVERT: N 261 GLN cc_start: 0.8033 (mp-120) cc_final: 0.7712 (mp-120) REVERT: M 127 VAL cc_start: 0.7753 (t) cc_final: 0.7533 (p) REVERT: M 480 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7929 (tt0) REVERT: D 830 LEU cc_start: 0.7096 (pp) cc_final: 0.6510 (mp) REVERT: D 868 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7930 (tppt) REVERT: D 995 ARG cc_start: 0.6442 (ttt180) cc_final: 0.5520 (mtp180) REVERT: D 1253 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7786 (m-10) REVERT: D 1465 TYR cc_start: 0.4173 (OUTLIER) cc_final: 0.3551 (t80) REVERT: D 1548 TRP cc_start: 0.9002 (OUTLIER) cc_final: 0.6978 (t-100) REVERT: D 1573 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8812 (tt) REVERT: A 189 MET cc_start: 0.6885 (tmm) cc_final: 0.6388 (tmm) REVERT: A 266 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6430 (m-10) REVERT: C 67 MET cc_start: 0.2230 (mmt) cc_final: 0.0863 (tmm) REVERT: C 269 TYR cc_start: 0.2741 (m-80) cc_final: 0.2494 (m-80) REVERT: C 359 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7861 (p90) outliers start: 63 outliers final: 47 residues processed: 225 average time/residue: 0.2757 time to fit residues: 98.9942 Evaluate side-chains 219 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 164 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 52 ASN Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 73 HIS Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 118 PHE Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 395 VAL Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 480 GLN Chi-restraints excluded: chain M residue 550 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 815 VAL Chi-restraints excluded: chain D residue 989 PHE Chi-restraints excluded: chain D residue 1212 HIS Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1364 THR Chi-restraints excluded: chain D residue 1414 PHE Chi-restraints excluded: chain D residue 1419 VAL Chi-restraints excluded: chain D residue 1465 TYR Chi-restraints excluded: chain D residue 1469 MET Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1543 ARG Chi-restraints excluded: chain D residue 1548 TRP Chi-restraints excluded: chain D residue 1573 LEU Chi-restraints excluded: chain D residue 1584 ASP Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 359 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 204 optimal weight: 10.0000 chunk 215 optimal weight: 0.0070 chunk 196 optimal weight: 0.9980 chunk 209 optimal weight: 20.0000 chunk 125 optimal weight: 0.4980 chunk 91 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 189 optimal weight: 0.0470 chunk 197 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 300 GLN M 315 HIS ** D 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN C 111 ASN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19413 Z= 0.164 Angle : 0.718 12.671 26293 Z= 0.354 Chirality : 0.044 0.222 2937 Planarity : 0.006 0.121 3363 Dihedral : 6.794 86.071 2572 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.38 % Favored : 86.58 % Rotamer: Outliers : 2.93 % Allowed : 19.52 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.23 % 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: -2.83 (0.17), residues: 2302 helix: 0.25 (0.19), residues: 772 sheet: -1.60 (0.25), residues: 396 loop : -3.69 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 173 HIS 0.009 0.001 HIS D1375 PHE 0.017 0.001 PHE D1289 TYR 0.027 0.001 TYR D 770 ARG 0.006 0.000 ARG C 348 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 190 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 73 HIS cc_start: 0.7776 (OUTLIER) cc_final: 0.7130 (t-90) REVERT: N 132 MET cc_start: 0.8888 (mtm) cc_final: 0.8563 (mtm) REVERT: N 261 GLN cc_start: 0.7928 (mp-120) cc_final: 0.7703 (mp-120) REVERT: M 250 ARG cc_start: 0.5012 (tmt90) cc_final: 0.4635 (ttp80) REVERT: M 499 LEU cc_start: 0.8177 (mt) cc_final: 0.7685 (tp) REVERT: D 995 ARG cc_start: 0.6016 (ttt180) cc_final: 0.5229 (mtp180) REVERT: D 1253 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7946 (m-10) REVERT: D 1405 TRP cc_start: 0.7956 (p90) cc_final: 0.6304 (m-10) REVERT: D 1465 TYR cc_start: 0.4712 (OUTLIER) cc_final: 0.3996 (t80) REVERT: D 1548 TRP cc_start: 0.9025 (OUTLIER) cc_final: 0.6809 (t-100) REVERT: D 1573 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8656 (tt) REVERT: A 1 MET cc_start: 0.3680 (ttt) cc_final: 0.3469 (ttt) REVERT: A 91 VAL cc_start: 0.8673 (t) cc_final: 0.8439 (p) REVERT: A 189 MET cc_start: 0.6875 (tmm) cc_final: 0.6309 (tmm) REVERT: A 252 MET cc_start: 0.6479 (ppp) cc_final: 0.6236 (ppp) REVERT: A 266 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6438 (m-10) REVERT: A 271 TYR cc_start: 0.7135 (m-80) cc_final: 0.6814 (m-80) REVERT: A 273 MET cc_start: 0.7493 (tmm) cc_final: 0.6753 (tpt) REVERT: C 67 MET cc_start: 0.1905 (mmt) cc_final: 0.0689 (tmm) REVERT: C 269 TYR cc_start: 0.3361 (m-80) cc_final: 0.3069 (m-80) REVERT: C 359 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7815 (p90) outliers start: 62 outliers final: 39 residues processed: 240 average time/residue: 0.3029 time to fit residues: 114.1058 Evaluate side-chains 211 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 165 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 73 HIS Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 118 PHE Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 395 VAL Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 439 LEU Chi-restraints excluded: chain M residue 480 GLN Chi-restraints excluded: chain M residue 550 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 815 VAL Chi-restraints excluded: chain D residue 1212 HIS Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1364 THR Chi-restraints excluded: chain D residue 1414 PHE Chi-restraints excluded: chain D residue 1419 VAL Chi-restraints excluded: chain D residue 1465 TYR Chi-restraints excluded: chain D residue 1469 MET Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1548 TRP Chi-restraints excluded: chain D residue 1573 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 359 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 137 optimal weight: 6.9990 chunk 221 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 213 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 113 optimal weight: 0.0020 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 52 ASN M 315 HIS D 289 GLN ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19413 Z= 0.168 Angle : 0.725 12.862 26293 Z= 0.357 Chirality : 0.044 0.216 2937 Planarity : 0.006 0.124 3363 Dihedral : 6.698 87.019 2572 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.16 % Favored : 86.79 % Rotamer: Outliers : 2.41 % Allowed : 20.46 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.23 % 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: -2.72 (0.17), residues: 2302 helix: 0.33 (0.20), residues: 773 sheet: -1.50 (0.25), residues: 389 loop : -3.62 (0.16), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 173 HIS 0.014 0.001 HIS D1375 PHE 0.021 0.001 PHE N 282 TYR 0.038 0.001 TYR D1487 ARG 0.007 0.000 ARG C 348 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 183 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 73 HIS cc_start: 0.7793 (OUTLIER) cc_final: 0.6837 (t-90) REVERT: N 261 GLN cc_start: 0.7942 (mp-120) cc_final: 0.7706 (mp-120) REVERT: M 121 MET cc_start: 0.4852 (pmm) cc_final: 0.3062 (mtp) REVERT: M 397 MET cc_start: 0.8406 (mtp) cc_final: 0.8145 (mtp) REVERT: D 148 ASN cc_start: 0.7013 (t0) cc_final: 0.6704 (t0) REVERT: D 861 HIS cc_start: 0.7142 (m-70) cc_final: 0.6581 (m90) REVERT: D 868 LYS cc_start: 0.8485 (ttpt) cc_final: 0.7927 (tppt) REVERT: D 995 ARG cc_start: 0.5946 (ttt180) cc_final: 0.5049 (mtp180) REVERT: D 1253 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7884 (m-10) REVERT: D 1377 ASN cc_start: 0.7777 (m-40) cc_final: 0.6888 (t0) REVERT: D 1405 TRP cc_start: 0.8111 (p90) cc_final: 0.6365 (m-10) REVERT: D 1465 TYR cc_start: 0.5272 (OUTLIER) cc_final: 0.4435 (t80) REVERT: D 1548 TRP cc_start: 0.8981 (OUTLIER) cc_final: 0.6945 (t-100) REVERT: D 1573 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8669 (tt) REVERT: A 91 VAL cc_start: 0.8651 (t) cc_final: 0.8414 (p) REVERT: A 132 VAL cc_start: 0.7077 (OUTLIER) cc_final: 0.6838 (m) REVERT: A 189 MET cc_start: 0.6904 (tmm) cc_final: 0.6353 (tmm) REVERT: A 223 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7202 (mtt-85) REVERT: A 252 MET cc_start: 0.6662 (ppp) cc_final: 0.6445 (ppp) REVERT: A 266 PHE cc_start: 0.7146 (OUTLIER) cc_final: 0.6441 (m-10) REVERT: A 273 MET cc_start: 0.7486 (tmm) cc_final: 0.7097 (tpt) REVERT: A 289 ASN cc_start: 0.7555 (m-40) cc_final: 0.6723 (t0) REVERT: C 67 MET cc_start: 0.2340 (mmt) cc_final: 0.0447 (tmm) REVERT: C 269 TYR cc_start: 0.2808 (m-80) cc_final: 0.2484 (m-80) REVERT: C 359 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7823 (p90) outliers start: 51 outliers final: 36 residues processed: 224 average time/residue: 0.2796 time to fit residues: 100.1025 Evaluate side-chains 214 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 169 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 52 ASN Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 73 HIS Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 87 PHE Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain N residue 118 PHE Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 369 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 211 LEU Chi-restraints excluded: chain M residue 243 ILE Chi-restraints excluded: chain M residue 395 VAL Chi-restraints excluded: chain M residue 439 LEU Chi-restraints excluded: chain M residue 480 GLN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 1212 HIS Chi-restraints excluded: chain D residue 1253 TYR Chi-restraints excluded: chain D residue 1364 THR Chi-restraints excluded: chain D residue 1414 PHE Chi-restraints excluded: chain D residue 1419 VAL Chi-restraints excluded: chain D residue 1465 TYR Chi-restraints excluded: chain D residue 1469 MET Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1548 TRP Chi-restraints excluded: chain D residue 1573 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain C residue 359 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 146 optimal weight: 9.9990 chunk 196 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 185 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 23 optimal weight: 0.0010 chunk 34 optimal weight: 2.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 52 ASN M 315 HIS M 405 GLN ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** 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 = 0.3946 r_free = 0.3946 target = 0.118833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.101882 restraints weight = 64046.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.101413 restraints weight = 55586.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.102101 restraints weight = 46524.812| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19413 Z= 0.199 Angle : 0.750 16.020 26293 Z= 0.368 Chirality : 0.045 0.254 2937 Planarity : 0.006 0.126 3363 Dihedral : 6.782 87.072 2572 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.99 % Favored : 85.97 % Rotamer: Outliers : 2.55 % Allowed : 20.42 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.23 % 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: -2.71 (0.17), residues: 2302 helix: 0.37 (0.20), residues: 774 sheet: -1.51 (0.25), residues: 396 loop : -3.66 (0.16), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 173 HIS 0.014 0.001 HIS D1375 PHE 0.017 0.001 PHE D1289 TYR 0.038 0.001 TYR D1487 ARG 0.014 0.000 ARG D 843 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3306.65 seconds wall clock time: 62 minutes 48.40 seconds (3768.40 seconds total)