Starting phenix.real_space_refine (version: dev) on Tue Apr 5 13:35:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2s_20579/04_2022/6q2s_20579_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2s_20579/04_2022/6q2s_20579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2s_20579/04_2022/6q2s_20579.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2s_20579/04_2022/6q2s_20579.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2s_20579/04_2022/6q2s_20579_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2s_20579/04_2022/6q2s_20579_neut.pdb" } resolution = 3.8 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= 0.007 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 "A ARG 146": "NH1" <-> "NH2" Residue "E TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "F TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 13726 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 743 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 8, 'TRANS': 89} Chain: "C" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1527 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain: "E" Number of atoms: 4491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4491 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 33, 'TRANS': 535, 'PCIS': 1} Chain breaks: 5 Chain: "B" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 743 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 8, 'TRANS': 89} Chain: "D" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1527 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain: "F" Number of atoms: 4491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4491 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 33, 'TRANS': 535, 'PCIS': 1} Chain breaks: 5 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Unusual residues: {' CA': 4, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Unusual residues: {' CA': 4, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 8.11, per 1000 atoms: 0.59 Number of scatterers: 13726 At special positions: 0 Unit cell: (133.75, 209.72, 75.97, 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) Ca 8 19.99 S 124 16.00 O 2570 8.00 N 2466 7.00 C 8558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A 123 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 216 " distance=2.02 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 218 " distance=2.02 Simple disulfide: pdb=" SG CYS A 187 " - pdb=" SG CYS B 187 " distance=2.05 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 218 " distance=2.02 Simple disulfide: pdb=" SG CYS C 169 " - pdb=" SG CYS C 175 " distance=2.02 Simple disulfide: pdb=" SG CYS C 186 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 248 " - pdb=" SG CYS C 316 " distance=2.04 Simple disulfide: pdb=" SG CYS C 255 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS C 272 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 328 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 142 " distance=2.02 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 197 " distance=2.03 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 243 " distance=2.03 Simple disulfide: pdb=" SG CYS E 426 " - pdb=" SG CYS E 430 " distance=2.02 Simple disulfide: pdb=" SG CYS E 449 " - pdb=" SG CYS E 478 " distance=2.03 Simple disulfide: pdb=" SG CYS E 515 " - pdb=" SG CYS E 531 " distance=2.03 Simple disulfide: pdb=" SG CYS E 519 " - pdb=" SG CYS E 541 " distance=2.03 Simple disulfide: pdb=" SG CYS E 528 " - pdb=" SG CYS E 558 " distance=2.02 Simple disulfide: pdb=" SG CYS E 565 " - pdb=" SG CYS E 581 " distance=2.02 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 585 " distance=2.03 Simple disulfide: pdb=" SG CYS E 609 " - pdb=" SG CYS E 620 " distance=2.04 Simple disulfide: pdb=" SG CYS E 611 " - pdb=" SG CYS E 618 " distance=2.03 Simple disulfide: pdb=" SG CYS B 123 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 216 " distance=2.02 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 218 " distance=2.02 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 218 " distance=2.02 Simple disulfide: pdb=" SG CYS D 169 " - pdb=" SG CYS D 175 " distance=2.02 Simple disulfide: pdb=" SG CYS D 186 " - pdb=" SG CYS D 196 " distance=2.02 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 248 " - pdb=" SG CYS D 316 " distance=2.04 Simple disulfide: pdb=" SG CYS D 255 " - pdb=" SG CYS D 261 " distance=2.03 Simple disulfide: pdb=" SG CYS D 272 " - pdb=" SG CYS D 288 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 328 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS F 142 " distance=2.02 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS F 166 " - pdb=" SG CYS F 243 " distance=2.03 Simple disulfide: pdb=" SG CYS F 426 " - pdb=" SG CYS F 430 " distance=2.02 Simple disulfide: pdb=" SG CYS F 449 " - pdb=" SG CYS F 478 " distance=2.03 Simple disulfide: pdb=" SG CYS F 515 " - pdb=" SG CYS F 531 " distance=2.03 Simple disulfide: pdb=" SG CYS F 519 " - pdb=" SG CYS F 541 " distance=2.03 Simple disulfide: pdb=" SG CYS F 528 " - pdb=" SG CYS F 558 " distance=2.02 Simple disulfide: pdb=" SG CYS F 565 " - pdb=" SG CYS F 581 " distance=2.02 Simple disulfide: pdb=" SG CYS F 570 " - pdb=" SG CYS F 585 " distance=2.03 Simple disulfide: pdb=" SG CYS F 609 " - pdb=" SG CYS F 620 " distance=2.04 Simple disulfide: pdb=" SG CYS F 611 " - pdb=" SG CYS F 618 " distance=2.03 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 Links applied NAG-ASN " NAG C1100 " - " ASN C 309 " " NAG D1100 " - " ASN D 309 " " NAG E 701 " - " ASN E 336 " " NAG E 702 " - " ASN E 377 " " NAG E 703 " - " ASN E 394 " " NAG E 704 " - " ASN E 468 " " NAG E 705 " - " ASN E 98 " " NAG E 706 " - " ASN E 361 " " NAG F 701 " - " ASN F 336 " " NAG F 702 " - " ASN F 377 " " NAG F 703 " - " ASN F 394 " " NAG F 704 " - " ASN F 468 " " NAG F 705 " - " ASN F 98 " " NAG F 706 " - " ASN F 361 " Time building additional restraints: 5.46 Conformation dependent library (CDL) restraints added in 2.2 seconds 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3256 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 36 sheets defined 23.4% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 133 through 136 removed outlier: 3.742A pdb=" N GLY A 136 " --> pdb=" O ARG A 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 133 through 136' Processing helix chain 'A' and resid 159 through 169 removed outlier: 3.521A pdb=" N LEU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 171 removed outlier: 3.614A pdb=" N LYS C 164 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA C 166 " --> pdb=" O CYS C 162 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS C 169 " --> pdb=" O PHE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 184 removed outlier: 3.653A pdb=" N ASP C 176 " --> pdb=" O ASN C 172 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 206 removed outlier: 3.689A pdb=" N THR C 202 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 217 removed outlier: 3.600A pdb=" N GLY C 214 " --> pdb=" O PRO C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 removed outlier: 3.647A pdb=" N GLY C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG C 230 " --> pdb=" O GLY C 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG C 231 " --> pdb=" O CYS C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 249 through 258 removed outlier: 3.635A pdb=" N ASP C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 272 removed outlier: 3.592A pdb=" N ASP C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 268 " --> pdb=" O ARG C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 293 removed outlier: 3.981A pdb=" N ARG C 290 " --> pdb=" O SER C 286 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 325 through 337 removed outlier: 3.867A pdb=" N LEU C 331 " --> pdb=" O GLU C 327 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 356 removed outlier: 3.752A pdb=" N GLN C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE C 356 " --> pdb=" O HIS C 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 109 Processing helix chain 'E' and resid 156 through 160 removed outlier: 3.503A pdb=" N SER E 159 " --> pdb=" O ALA E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 167 removed outlier: 3.641A pdb=" N CYS E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE E 167 " --> pdb=" O ARG E 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 162 through 167' Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 309 through 314 removed outlier: 3.782A pdb=" N ARG E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 329 removed outlier: 3.873A pdb=" N GLN E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 522 removed outlier: 3.786A pdb=" N VAL E 521 " --> pdb=" O SER E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 530 removed outlier: 3.706A pdb=" N GLU E 529 " --> pdb=" O ARG E 525 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 525 through 530' Processing helix chain 'E' and resid 581 through 585 removed outlier: 3.786A pdb=" N ASP E 584 " --> pdb=" O CYS E 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 136 removed outlier: 3.742A pdb=" N GLY B 136 " --> pdb=" O ARG B 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 133 through 136' Processing helix chain 'B' and resid 159 through 169 removed outlier: 3.521A pdb=" N LEU B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 171 removed outlier: 3.613A pdb=" N LYS D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA D 166 " --> pdb=" O CYS D 162 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS D 169 " --> pdb=" O PHE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 184 removed outlier: 3.653A pdb=" N ASP D 176 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG D 177 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 206 removed outlier: 3.690A pdb=" N THR D 202 " --> pdb=" O ARG D 198 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 217 removed outlier: 3.600A pdb=" N GLY D 214 " --> pdb=" O PRO D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 removed outlier: 3.647A pdb=" N GLY D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG D 230 " --> pdb=" O GLY D 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG D 231 " --> pdb=" O CYS D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 241 Processing helix chain 'D' and resid 249 through 258 removed outlier: 3.635A pdb=" N ASP D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.592A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 293 removed outlier: 3.981A pdb=" N ARG D 290 " --> pdb=" O SER D 286 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 296 No H-bonds generated for 'chain 'D' and resid 294 through 296' Processing helix chain 'D' and resid 325 through 337 removed outlier: 3.866A pdb=" N LEU D 331 " --> pdb=" O GLU D 327 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 356 removed outlier: 3.752A pdb=" N GLN D 354 " --> pdb=" O ARG D 350 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE D 356 " --> pdb=" O HIS D 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 109 Processing helix chain 'F' and resid 156 through 160 removed outlier: 3.503A pdb=" N SER F 159 " --> pdb=" O ALA F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 removed outlier: 3.642A pdb=" N CYS F 166 " --> pdb=" O PRO F 162 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 162 through 167' Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 309 through 314 removed outlier: 3.782A pdb=" N ARG F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 329 removed outlier: 3.873A pdb=" N GLN F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 522 removed outlier: 3.786A pdb=" N VAL F 521 " --> pdb=" O SER F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 530 removed outlier: 3.707A pdb=" N GLU F 529 " --> pdb=" O ARG F 525 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU F 530 " --> pdb=" O LEU F 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 525 through 530' Processing helix chain 'F' and resid 581 through 585 removed outlier: 3.786A pdb=" N ASP F 584 " --> pdb=" O CYS F 581 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 125 removed outlier: 3.551A pdb=" N SER A 151 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 187 through 199 removed outlier: 6.959A pdb=" N CYS A 188 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N CYS A 218 " --> pdb=" O CYS A 188 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N CYS A 216 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG A 192 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL A 196 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG A 210 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE A 198 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL A 208 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 303 through 304 Processing sheet with id=AA5, first strand: chain 'E' and resid 30 through 31 removed outlier: 3.578A pdb=" N TYR E 30 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.515A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU E 40 " --> pdb=" O PHE E 150 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR E 152 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.515A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 48 through 52 removed outlier: 3.924A pdb=" N THR E 48 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU E 95 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 174 through 176 removed outlier: 3.576A pdb=" N THR E 261 " --> pdb=" O PHE E 174 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL E 256 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA E 241 " --> pdb=" O VAL E 256 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 184 through 187 removed outlier: 6.665A pdb=" N THR E 184 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N THR E 225 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS E 186 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 292 through 300 removed outlier: 4.064A pdb=" N ALA E 294 " --> pdb=" O LEU E 356 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP E 353 " --> pdb=" O TRP E 334 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP E 334 " --> pdb=" O ASP E 353 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 316 through 318 removed outlier: 3.734A pdb=" N VAL E 395 " --> pdb=" O MET E 370 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 407 through 413 removed outlier: 7.220A pdb=" N TYR E 408 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR E 503 " --> pdb=" O TYR E 408 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU E 410 " --> pdb=" O THR E 503 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLU E 505 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL E 412 " --> pdb=" O GLU E 505 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU E 500 " --> pdb=" O TYR E 483 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR E 483 " --> pdb=" O LEU E 500 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 407 through 413 removed outlier: 7.220A pdb=" N TYR E 408 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR E 503 " --> pdb=" O TYR E 408 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU E 410 " --> pdb=" O THR E 503 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLU E 505 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL E 412 " --> pdb=" O GLU E 505 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL E 502 " --> pdb=" O LEU E 481 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU E 481 " --> pdb=" O VAL E 502 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 421 through 425 removed outlier: 7.346A pdb=" N GLN E 421 " --> pdb=" O VAL E 467 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL E 467 " --> pdb=" O GLN E 421 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY E 423 " --> pdb=" O LEU E 465 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU E 465 " --> pdb=" O GLY E 423 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER E 462 " --> pdb=" O SER E 457 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 542 through 544 Processing sheet with id=AB8, first strand: chain 'E' and resid 551 through 552 removed outlier: 4.345A pdb=" N THR E 552 " --> pdb=" O GLY E 605 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY E 605 " --> pdb=" O THR E 552 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 589 through 591 removed outlier: 6.519A pdb=" N SER E 589 " --> pdb=" O CYS E 618 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N CYS E 620 " --> pdb=" O SER E 589 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL E 591 " --> pdb=" O CYS E 620 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 124 through 125 removed outlier: 3.552A pdb=" N SER B 151 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 128 through 131 Processing sheet with id=AC3, first strand: chain 'B' and resid 187 through 199 removed outlier: 6.959A pdb=" N CYS B 188 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N CYS B 218 " --> pdb=" O CYS B 188 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N CYS B 216 " --> pdb=" O PRO B 190 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG B 192 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL B 196 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG B 210 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE B 198 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL B 208 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 303 through 304 Processing sheet with id=AC5, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.578A pdb=" N TYR F 30 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.514A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU F 40 " --> pdb=" O PHE F 150 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR F 152 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.514A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 48 through 52 removed outlier: 3.924A pdb=" N THR F 48 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU F 95 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 174 through 176 removed outlier: 3.576A pdb=" N THR F 261 " --> pdb=" O PHE F 174 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL F 256 " --> pdb=" O ALA F 241 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA F 241 " --> pdb=" O VAL F 256 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 184 through 187 removed outlier: 6.664A pdb=" N THR F 184 " --> pdb=" O THR F 225 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N THR F 225 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS F 186 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 292 through 300 removed outlier: 4.063A pdb=" N ALA F 294 " --> pdb=" O LEU F 356 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP F 353 " --> pdb=" O TRP F 334 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP F 334 " --> pdb=" O ASP F 353 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 316 through 318 removed outlier: 3.734A pdb=" N VAL F 395 " --> pdb=" O MET F 370 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 407 through 413 removed outlier: 7.220A pdb=" N TYR F 408 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR F 503 " --> pdb=" O TYR F 408 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU F 410 " --> pdb=" O THR F 503 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLU F 505 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL F 412 " --> pdb=" O GLU F 505 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU F 500 " --> pdb=" O TYR F 483 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR F 483 " --> pdb=" O LEU F 500 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 407 through 413 removed outlier: 7.220A pdb=" N TYR F 408 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR F 503 " --> pdb=" O TYR F 408 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU F 410 " --> pdb=" O THR F 503 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLU F 505 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL F 412 " --> pdb=" O GLU F 505 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL F 502 " --> pdb=" O LEU F 481 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU F 481 " --> pdb=" O VAL F 502 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 421 through 425 removed outlier: 7.346A pdb=" N GLN F 421 " --> pdb=" O VAL F 467 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL F 467 " --> pdb=" O GLN F 421 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY F 423 " --> pdb=" O LEU F 465 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU F 465 " --> pdb=" O GLY F 423 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER F 462 " --> pdb=" O SER F 457 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AD8, first strand: chain 'F' and resid 551 through 552 removed outlier: 4.345A pdb=" N THR F 552 " --> pdb=" O GLY F 605 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY F 605 " --> pdb=" O THR F 552 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 589 through 591 removed outlier: 6.520A pdb=" N SER F 589 " --> pdb=" O CYS F 618 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N CYS F 620 " --> pdb=" O SER F 589 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL F 591 " --> pdb=" O CYS F 620 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 948 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: 4.13 Time building geometry restraints manager: 5.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4593 1.34 - 1.47: 3334 1.47 - 1.59: 5949 1.59 - 1.72: 0 1.72 - 1.84: 142 Bond restraints: 14018 Sorted by residual: bond pdb=" C CYS F 565 " pdb=" N PRO F 566 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.09e+00 bond pdb=" C CYS E 565 " pdb=" N PRO E 566 " ideal model delta sigma weight residual 1.334 1.391 -0.058 2.34e-02 1.83e+03 6.04e+00 bond pdb=" N ASP E 584 " pdb=" CA ASP E 584 " ideal model delta sigma weight residual 1.458 1.438 0.020 9.00e-03 1.23e+04 4.85e+00 bond pdb=" N ASP F 584 " pdb=" CA ASP F 584 " ideal model delta sigma weight residual 1.458 1.438 0.020 9.00e-03 1.23e+04 4.83e+00 bond pdb=" CG ASN F 361 " pdb=" ND2 ASN F 361 " ideal model delta sigma weight residual 1.328 1.366 -0.038 2.10e-02 2.27e+03 3.20e+00 ... (remaining 14013 not shown) Histogram of bond angle deviations from ideal: 99.50 - 107.01: 594 107.01 - 114.51: 8063 114.51 - 122.01: 7386 122.01 - 129.52: 2873 129.52 - 137.02: 102 Bond angle restraints: 19018 Sorted by residual: angle pdb=" C VAL F 427 " pdb=" N GLU F 428 " pdb=" CA GLU F 428 " ideal model delta sigma weight residual 120.38 127.46 -7.08 1.46e+00 4.69e-01 2.35e+01 angle pdb=" C VAL E 427 " pdb=" N GLU E 428 " pdb=" CA GLU E 428 " ideal model delta sigma weight residual 120.38 127.45 -7.07 1.46e+00 4.69e-01 2.35e+01 angle pdb=" C TYR E 76 " pdb=" N ARG E 77 " pdb=" CA ARG E 77 " ideal model delta sigma weight residual 121.54 129.60 -8.06 1.91e+00 2.74e-01 1.78e+01 angle pdb=" C TYR F 76 " pdb=" N ARG F 77 " pdb=" CA ARG F 77 " ideal model delta sigma weight residual 121.54 129.57 -8.03 1.91e+00 2.74e-01 1.77e+01 angle pdb=" N VAL E 304 " pdb=" CA VAL E 304 " pdb=" C VAL E 304 " ideal model delta sigma weight residual 108.88 116.52 -7.64 2.16e+00 2.14e-01 1.25e+01 ... (remaining 19013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 8298 17.62 - 35.24: 263 35.24 - 52.86: 34 52.86 - 70.49: 0 70.49 - 88.11: 4 Dihedral angle restraints: 8599 sinusoidal: 3581 harmonic: 5018 Sorted by residual: dihedral pdb=" CB CYS E 515 " pdb=" SG CYS E 515 " pdb=" SG CYS E 531 " pdb=" CB CYS E 531 " ideal model delta sinusoidal sigma weight residual 93.00 -178.89 -88.11 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS F 515 " pdb=" SG CYS F 515 " pdb=" SG CYS F 531 " pdb=" CB CYS F 531 " ideal model delta sinusoidal sigma weight residual 93.00 -178.90 -88.10 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS F 426 " pdb=" SG CYS F 426 " pdb=" SG CYS F 430 " pdb=" CB CYS F 430 " ideal model delta sinusoidal sigma weight residual -86.00 -168.97 82.97 1 1.00e+01 1.00e-02 8.43e+01 ... (remaining 8596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2118 0.132 - 0.264: 32 0.264 - 0.396: 2 0.396 - 0.528: 0 0.528 - 0.660: 4 Chirality restraints: 2156 Sorted by residual: chirality pdb=" C1 NAG E 704 " pdb=" ND2 ASN E 468 " pdb=" C2 NAG E 704 " pdb=" O5 NAG E 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" C1 NAG F 704 " pdb=" ND2 ASN F 468 " pdb=" C2 NAG F 704 " pdb=" O5 NAG F 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" C1 NAG F 702 " pdb=" ND2 ASN F 377 " pdb=" C2 NAG F 702 " pdb=" O5 NAG F 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.51e+00 ... (remaining 2153 not shown) Planarity restraints: 2492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 59 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.52e+00 pdb=" N PRO E 60 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 60 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 60 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 59 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO F 60 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO F 60 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 60 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 258 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO D 259 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 259 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 259 " 0.033 5.00e-02 4.00e+02 ... (remaining 2489 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.07: 12 2.07 - 2.78: 2967 2.78 - 3.49: 16353 3.49 - 4.19: 30175 4.19 - 4.90: 51736 Nonbonded interactions: 101243 Sorted by model distance: nonbonded pdb=" OD2 ASP F 300 " pdb=" OH TYR F 314 " model vdw 1.366 2.440 nonbonded pdb=" OD2 ASP E 300 " pdb=" OH TYR E 314 " model vdw 1.367 2.440 nonbonded pdb=" OD1 ASP E 266 " pdb=" OD2 ASP E 302 " model vdw 1.613 3.040 nonbonded pdb=" OD1 ASP F 266 " pdb=" OD2 ASP F 302 " model vdw 1.613 3.040 nonbonded pdb=" O THR F 564 " pdb=" OD2 ASP F 567 " model vdw 1.692 3.040 ... (remaining 101238 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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 Ca 8 9.91 5 S 124 5.16 5 C 8558 2.51 5 N 2466 2.21 5 O 2570 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: 0.530 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: 0.010 Extract box with map and model: 4.350 Check model and map are aligned: 0.230 Convert atoms to be neutral: 0.130 Process input model: 37.680 Find NCS groups from input model: 0.710 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5080 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 0.061 14018 Z= 0.500 Angle : 1.051 15.609 19018 Z= 0.578 Chirality : 0.061 0.660 2156 Planarity : 0.007 0.069 2478 Dihedral : 8.584 44.829 5196 Min Nonbonded Distance : 1.366 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.58 (0.15), residues: 1702 helix: -4.22 (0.13), residues: 320 sheet: -2.35 (0.23), residues: 434 loop : -3.01 (0.15), residues: 948 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 417 time to evaluate : 1.654 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: symmetry clash outliers start: 2 outliers final: 0 residues processed: 419 average time/residue: 0.3476 time to fit residues: 194.6873 Evaluate side-chains 167 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.721 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 30.0000 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 68 optimal weight: 30.0000 chunk 133 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS C 194 HIS ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 338 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN E 103 HIS ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 HIS E 403 HIS E 443 HIS ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 HIS ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 HIS ** F 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.093 14018 Z= 0.371 Angle : 0.884 11.136 19018 Z= 0.451 Chirality : 0.052 0.469 2156 Planarity : 0.008 0.120 2478 Dihedral : 6.232 26.519 1992 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 4.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.17), residues: 1702 helix: -3.03 (0.21), residues: 344 sheet: -1.91 (0.24), residues: 436 loop : -2.78 (0.16), residues: 922 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 186 time to evaluate : 1.682 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: 63 outliers final: 39 residues processed: 232 average time/residue: 0.2437 time to fit residues: 84.4648 Evaluate side-chains 177 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 138 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.1371 time to fit residues: 11.5701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 HIS D 323 ASN ** D 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 HIS F 84 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.8147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.105 14018 Z= 0.429 Angle : 0.924 11.069 19018 Z= 0.471 Chirality : 0.053 0.533 2156 Planarity : 0.008 0.095 2478 Dihedral : 6.601 28.218 1992 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer Outliers : 4.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.17), residues: 1702 helix: -2.76 (0.23), residues: 342 sheet: -1.87 (0.24), residues: 418 loop : -2.82 (0.17), residues: 942 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 165 time to evaluate : 1.847 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: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 35 residues processed: 214 average time/residue: 0.2464 time to fit residues: 78.6764 Evaluate side-chains 155 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 120 time to evaluate : 1.540 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1464 time to fit residues: 11.1146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 164 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** C 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 HIS ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 439 GLN ** F 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.8394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.111 14018 Z= 0.213 Angle : 0.698 10.602 19018 Z= 0.342 Chirality : 0.045 0.331 2156 Planarity : 0.007 0.125 2478 Dihedral : 5.401 23.337 1992 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.18), residues: 1702 helix: -2.10 (0.25), residues: 328 sheet: -1.38 (0.24), residues: 430 loop : -2.46 (0.18), residues: 944 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 181 average time/residue: 0.2588 time to fit residues: 69.0273 Evaluate side-chains 147 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.807 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1334 time to fit residues: 6.5688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 2 optimal weight: 0.5980 chunk 122 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 0 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 HIS ** D 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 439 GLN ** F 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.8903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.115 14018 Z= 0.212 Angle : 0.692 10.149 19018 Z= 0.339 Chirality : 0.045 0.343 2156 Planarity : 0.006 0.093 2478 Dihedral : 5.166 21.692 1992 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.19), residues: 1702 helix: -1.70 (0.27), residues: 330 sheet: -1.10 (0.24), residues: 430 loop : -2.29 (0.18), residues: 942 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 161 average time/residue: 0.2291 time to fit residues: 57.2225 Evaluate side-chains 141 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.725 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1366 time to fit residues: 5.6405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 96 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 164 optimal weight: 0.1980 chunk 136 optimal weight: 8.9990 chunk 76 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 86 optimal weight: 0.6980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN F 138 GLN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.9318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 14018 Z= 0.197 Angle : 0.655 9.983 19018 Z= 0.319 Chirality : 0.044 0.325 2156 Planarity : 0.006 0.110 2478 Dihedral : 4.949 21.097 1992 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.19), residues: 1702 helix: -1.28 (0.28), residues: 324 sheet: -0.93 (0.25), residues: 430 loop : -2.22 (0.18), residues: 948 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 163 average time/residue: 0.2189 time to fit residues: 56.4046 Evaluate side-chains 139 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 1.688 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1360 time to fit residues: 6.9074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 93 optimal weight: 0.0870 chunk 120 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 202 ASN D 352 HIS ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 439 GLN ** F 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 moved from start: 0.9883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.180 14018 Z= 0.250 Angle : 0.713 14.969 19018 Z= 0.358 Chirality : 0.046 0.359 2156 Planarity : 0.006 0.112 2478 Dihedral : 5.117 20.650 1992 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.19), residues: 1702 helix: -1.19 (0.28), residues: 332 sheet: -0.92 (0.25), residues: 432 loop : -2.18 (0.19), residues: 938 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 17 residues processed: 145 average time/residue: 0.2309 time to fit residues: 51.8743 Evaluate side-chains 133 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 1.698 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1472 time to fit residues: 6.4131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 GLN E 392 HIS ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 439 GLN ** F 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 1.0279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 14018 Z= 0.227 Angle : 0.693 10.907 19018 Z= 0.339 Chirality : 0.045 0.351 2156 Planarity : 0.005 0.088 2478 Dihedral : 5.026 21.304 1992 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.19), residues: 1702 helix: -1.07 (0.28), residues: 334 sheet: -0.84 (0.25), residues: 428 loop : -2.14 (0.19), residues: 940 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 136 average time/residue: 0.2340 time to fit residues: 49.7856 Evaluate side-chains 119 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 1.688 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1209 time to fit residues: 3.7816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 0.0670 chunk 46 optimal weight: 6.9990 chunk 137 optimal weight: 0.0980 chunk 144 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 overall best weight: 2.4324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 439 GLN ** F 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 1.0612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 14018 Z= 0.221 Angle : 0.695 10.176 19018 Z= 0.339 Chirality : 0.045 0.342 2156 Planarity : 0.005 0.079 2478 Dihedral : 4.977 21.453 1992 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.19), residues: 1702 helix: -1.00 (0.28), residues: 336 sheet: -0.92 (0.25), residues: 408 loop : -2.10 (0.19), residues: 958 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 136 average time/residue: 0.2435 time to fit residues: 50.2338 Evaluate side-chains 124 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 1.709 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1311 time to fit residues: 4.1608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.0070 chunk 76 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 82 optimal weight: 0.0770 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN F 439 GLN ** F 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 1.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 14018 Z= 0.187 Angle : 0.684 10.622 19018 Z= 0.328 Chirality : 0.045 0.297 2156 Planarity : 0.005 0.077 2478 Dihedral : 4.829 21.114 1992 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.46 % Favored : 94.48 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.20), residues: 1702 helix: -0.80 (0.29), residues: 332 sheet: -0.77 (0.26), residues: 414 loop : -2.00 (0.19), residues: 956 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 131 average time/residue: 0.2345 time to fit residues: 47.5184 Evaluate side-chains 120 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 1.676 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1249 time to fit residues: 3.4646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 chunk 56 optimal weight: 0.3980 chunk 138 optimal weight: 10.0000 chunk 17 optimal weight: 0.0000 chunk 24 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 GLN ** C 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS ** F 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.116499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.097391 restraints weight = 57296.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.099662 restraints weight = 33626.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.101194 restraints weight = 22742.863| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 1.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 14018 Z= 0.175 Angle : 0.660 9.453 19018 Z= 0.315 Chirality : 0.044 0.292 2156 Planarity : 0.005 0.074 2478 Dihedral : 4.606 20.472 1992 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.20), residues: 1702 helix: -0.65 (0.29), residues: 332 sheet: -0.57 (0.26), residues: 412 loop : -1.90 (0.19), residues: 958 =============================================================================== Job complete usr+sys time: 2471.31 seconds wall clock time: 45 minutes 55.46 seconds (2755.46 seconds total)