Starting phenix.real_space_refine (version: dev) on Wed Apr 6 06:56:47 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ces_7464/04_2022/6ces_7464_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ces_7464/04_2022/6ces_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_7464/04_2022/6ces_7464.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ces_7464/04_2022/6ces_7464.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ces_7464/04_2022/6ces_7464_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ces_7464/04_2022/6ces_7464_neut_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Convert atoms to be neutral 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: 10.65, per 1000 atoms: 0.56 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: 7.59 Conformation dependent library (CDL) restraints added in 2.9 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: 2.04 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: 5.96 Time building geometry restraints manager: 8.23 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 - 15.40: 10586 15.40 - 30.81: 881 30.81 - 46.21: 210 46.21 - 61.61: 15 61.61 - 77.02: 8 Dihedral angle restraints: 11700 sinusoidal: 4775 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 11697 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 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. 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.650 Check model and map are aligned: 0.330 Convert atoms to be neutral: 0.180 Process input model: 48.100 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 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 : 12.092 77.017 7186 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.43 % Allowed : 16.77 % Favored : 82.80 % Rotamer Outliers : 0.99 % 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 *********************** 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 : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 5 residues processed: 324 average time/residue: 0.3595 time to fit residues: 171.6869 Evaluate side-chains 165 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 160 time to evaluate : 2.364 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1652 time to fit residues: 4.8079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 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: 4.9990 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 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 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: 0.7398 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 19413 Z= 0.271 Angle : 0.843 16.470 26293 Z= 0.435 Chirality : 0.047 0.251 2937 Planarity : 0.007 0.092 3363 Dihedral : 8.047 49.845 2538 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 15.38 % Favored : 84.54 % Rotamer Outliers : 2.84 % 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: -4.30 (0.15), residues: 2302 helix: -1.39 (0.17), residues: 757 sheet: -2.11 (0.24), residues: 406 loop : -4.35 (0.14), residues: 1139 *********************** 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 246 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 186 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 26 residues processed: 236 average time/residue: 0.2958 time to fit residues: 109.3299 Evaluate side-chains 177 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 2.524 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2046 time to fit residues: 12.6459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 117 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 144 optimal weight: 0.0870 chunk 58 optimal weight: 8.9990 chunk 211 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 overall best weight: 5.0166 ------------------------------------------------------------------------------- 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** M 339 ASN D 323 ASN D 797 GLN ** D 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1473 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.087 19413 Z= 0.475 Angle : 0.976 15.061 26293 Z= 0.507 Chirality : 0.052 0.273 2937 Planarity : 0.008 0.102 3363 Dihedral : 8.427 49.105 2538 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 18.20 % Favored : 81.67 % Rotamer Outliers : 3.50 % 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: -4.18 (0.15), residues: 2302 helix: -1.08 (0.18), residues: 754 sheet: -2.31 (0.23), residues: 405 loop : -4.32 (0.14), residues: 1143 *********************** 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 235 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 161 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 32 residues processed: 223 average time/residue: 0.2747 time to fit residues: 98.5867 Evaluate side-chains 174 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 2.426 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1693 time to fit residues: 13.3665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 209 optimal weight: 8.9990 chunk 159 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 201 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 205 HIS ** 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 355 GLN D 809 GLN ** D 820 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1406 HIS A 250 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.096 19413 Z= 0.260 Angle : 0.817 15.035 26293 Z= 0.416 Chirality : 0.046 0.236 2937 Planarity : 0.007 0.124 3363 Dihedral : 7.749 54.807 2538 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.94 % Favored : 84.97 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % 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: -3.76 (0.16), residues: 2302 helix: -0.57 (0.19), residues: 761 sheet: -2.06 (0.24), residues: 403 loop : -4.22 (0.15), residues: 1138 *********************** 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 214 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 170 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 15 residues processed: 205 average time/residue: 0.2784 time to fit residues: 91.7738 Evaluate side-chains 163 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 2.430 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1712 time to fit residues: 7.9340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 187 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 167 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 56 optimal weight: 0.0270 overall best weight: 1.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 205 HIS ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 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 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.998 19413 Z= 0.361 Angle : 1.082 106.085 26293 Z= 0.490 Chirality : 0.047 0.259 2937 Planarity : 0.007 0.114 3363 Dihedral : 7.702 54.845 2538 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 15.99 % Favored : 83.93 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % 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: -3.67 (0.16), residues: 2302 helix: -0.42 (0.19), residues: 762 sheet: -2.06 (0.24), residues: 397 loop : -4.19 (0.15), residues: 1143 *********************** 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 188 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 2.469 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 14 residues processed: 178 average time/residue: 0.2946 time to fit residues: 84.6009 Evaluate side-chains 164 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 2.448 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1949 time to fit residues: 7.9118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 75 optimal weight: 20.0000 chunk 202 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 225 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.235 19413 Z= 0.309 Angle : 0.838 19.141 26293 Z= 0.432 Chirality : 0.047 0.230 2937 Planarity : 0.007 0.096 3363 Dihedral : 7.587 54.514 2538 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 17.12 % Favored : 82.80 % Rotamer Outliers : 2.36 % 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: -3.56 (0.16), residues: 2302 helix: -0.28 (0.19), residues: 765 sheet: -2.05 (0.24), residues: 408 loop : -4.18 (0.15), residues: 1129 *********************** 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 213 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 163 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 23 residues processed: 207 average time/residue: 0.2801 time to fit residues: 93.0398 Evaluate side-chains 173 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 2.368 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2109 time to fit residues: 11.6128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 217 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 224 optimal weight: 0.0670 chunk 140 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.762 19413 Z= 0.543 Angle : 1.204 106.095 26293 Z= 0.566 Chirality : 0.047 0.459 2937 Planarity : 0.007 0.154 3363 Dihedral : 7.634 54.568 2538 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 17.25 % Favored : 82.58 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.80 % 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: -3.55 (0.16), residues: 2302 helix: -0.25 (0.19), residues: 765 sheet: -2.07 (0.24), residues: 408 loop : -4.17 (0.15), residues: 1129 *********************** 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 171 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 2.630 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 168 average time/residue: 0.3008 time to fit residues: 81.2967 Evaluate side-chains 154 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 2.460 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2264 time to fit residues: 5.8367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 138 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 67 optimal weight: 0.3980 chunk 44 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 142 optimal weight: 0.0170 chunk 153 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 overall best weight: 1.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.762 19413 Z= 0.636 Angle : 1.242 106.096 26293 Z= 0.606 Chirality : 0.047 0.459 2937 Planarity : 0.008 0.154 3363 Dihedral : 7.634 54.568 2538 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 17.25 % Favored : 82.58 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.80 % 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: -3.55 (0.16), residues: 2302 helix: -0.25 (0.19), residues: 765 sheet: -2.07 (0.24), residues: 408 loop : -4.17 (0.15), residues: 1129 *********************** 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 149 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 2.417 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 149 average time/residue: 0.3094 time to fit residues: 73.5550 Evaluate side-chains 148 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 2.553 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1829 time to fit residues: 3.5780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 204 optimal weight: 9.9990 chunk 215 optimal weight: 0.5980 chunk 196 optimal weight: 0.8980 chunk 209 optimal weight: 20.0000 chunk 125 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 189 optimal weight: 0.0770 chunk 197 optimal weight: 6.9990 chunk 208 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.762 19413 Z= 0.636 Angle : 1.242 106.100 26293 Z= 0.606 Chirality : 0.047 0.459 2937 Planarity : 0.008 0.154 3363 Dihedral : 7.634 54.568 2538 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 17.25 % Favored : 82.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.80 % 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: -3.55 (0.16), residues: 2302 helix: -0.25 (0.19), residues: 765 sheet: -2.07 (0.24), residues: 408 loop : -4.17 (0.15), residues: 1129 *********************** 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 148 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.428 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.3036 time to fit residues: 72.1652 Evaluate side-chains 147 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 2.761 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 137 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.762 19413 Z= 0.636 Angle : 1.242 106.100 26293 Z= 0.606 Chirality : 0.047 0.459 2937 Planarity : 0.008 0.154 3363 Dihedral : 7.634 54.568 2538 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 17.25 % Favored : 82.58 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.80 % 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: -3.55 (0.16), residues: 2302 helix: -0.25 (0.19), residues: 765 sheet: -2.07 (0.24), residues: 408 loop : -4.17 (0.15), residues: 1129 ********************** 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 148 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 2.363 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 148 average time/residue: 0.2953 time to fit residues: 70.3377 Evaluate side-chains 148 residues out of total 2118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 2.461 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1921 time to fit residues: 3.6624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 146 optimal weight: 10.0000 chunk 196 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 34 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.116142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.099685 restraints weight = 64786.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.099043 restraints weight = 54207.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.099779 restraints weight = 48027.110| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.762 19413 Z= 0.636 Angle : 1.242 106.100 26293 Z= 0.606 Chirality : 0.047 0.459 2937 Planarity : 0.008 0.154 3363 Dihedral : 7.634 54.568 2538 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 17.25 % Favored : 82.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.80 % 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: -3.55 (0.16), residues: 2302 helix: -0.25 (0.19), residues: 765 sheet: -2.07 (0.24), residues: 408 loop : -4.17 (0.15), residues: 1129 =============================================================================== Job complete usr+sys time: 2853.86 seconds wall clock time: 53 minutes 54.19 seconds (3234.19 seconds total)