Starting phenix.real_space_refine (version: dev) on Tue Feb 21 12:44:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qna_14072/02_2023/7qna_14072_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qna_14072/02_2023/7qna_14072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qna_14072/02_2023/7qna_14072.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qna_14072/02_2023/7qna_14072.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qna_14072/02_2023/7qna_14072_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qna_14072/02_2023/7qna_14072_updated.pdb" } resolution = 3.0 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= 0.000 sd= 0.003 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 Process input model Symmetric amino acids flipped Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14777 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2693 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 316} Chain breaks: 1 Chain: "B" Number of atoms: 2691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2752 Chain: "C" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2701 Classifications: {'peptide': 328} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 314} Chain breaks: 1 Chain: "D" Number of atoms: 2698 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2744 Chain: "E" Number of atoms: 2691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 327, 2686 Classifications: {'peptide': 327} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 bond proxies already assigned to first conformer: 2752 Chain: "N" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "A" 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: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} 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 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR D 66 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR D 66 " occ=0.50 Time building chain proxies: 11.50, per 1000 atoms: 0.78 Number of scatterers: 14777 At special positions: 0 Unit cell: (119.168, 92.288, 128.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 89 16.00 O 2700 8.00 N 2362 7.00 C 9626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS N 409 " - pdb=" SG CYS N 483 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA a 3 " - " MAN a 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A 601 " - " ASN A 157 " " NAG C 501 " - " ASN C 208 " " NAG F 1 " - " ASN B 149 " " NAG G 1 " - " ASN D 149 " " NAG H 1 " - " ASN E 149 " " NAG a 1 " - " ASN A 144 " " NAG b 1 " - " ASN B 80 " " NAG d 1 " - " ASN D 80 " " NAG e 1 " - " ASN E 80 " Time building additional restraints: 6.22 Conformation dependent library (CDL) restraints added in 3.3 seconds 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 24 sheets defined 35.5% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 49 through 56 Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.633A pdb=" N THR A 125 " --> pdb=" O MET A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 208 through 211 No H-bonds generated for 'chain 'A' and resid 208 through 211' Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 264 through 279 removed outlier: 4.265A pdb=" N SER A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TRP A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 308 Processing helix chain 'A' and resid 318 through 347 removed outlier: 3.507A pdb=" N ILE A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 543 removed outlier: 3.509A pdb=" N ILE A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Proline residue: A 527 - end of helix Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 226 through 241 removed outlier: 3.576A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 3.711A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 306 Processing helix chain 'B' and resid 423 through 446 Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 28 through 35 Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 100 through 105 removed outlier: 3.656A pdb=" N GLY C 104 " --> pdb=" O ASN C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 removed outlier: 3.652A pdb=" N ILE C 238 " --> pdb=" O GLY C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 256 removed outlier: 4.061A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TRP C 256 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 284 removed outlier: 3.516A pdb=" N THR C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 322 Processing helix chain 'C' and resid 410 through 434 removed outlier: 3.691A pdb=" N ILE C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.501A pdb=" N VAL C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 226 through 241 removed outlier: 3.576A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 271 removed outlier: 3.711A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR D 271 " --> pdb=" O HIS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 306 Processing helix chain 'D' and resid 423 through 446 Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 85 through 90 Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 226 through 241 removed outlier: 3.575A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TRP E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 271 removed outlier: 3.710A pdb=" N GLU E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR E 271 " --> pdb=" O HIS E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 306 Processing helix chain 'E' and resid 423 through 446 Proline residue: E 432 - end of helix Processing helix chain 'N' and resid 475 through 477 No H-bonds generated for 'chain 'N' and resid 475 through 477' Processing helix chain 'N' and resid 496 through 498 No H-bonds generated for 'chain 'N' and resid 496 through 498' Processing sheet with id= A, first strand: chain 'A' and resid 200 through 204 removed outlier: 6.336A pdb=" N THR A 72 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N THR A 203 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL A 74 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU A 73 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A 104 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASP A 96 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N PHE A 83 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR A 94 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR A 159 " --> pdb=" O MET A 155 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 78 through 80 Processing sheet with id= C, first strand: chain 'A' and resid 132 through 134 removed outlier: 4.266A pdb=" N SER A 192 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE A 244 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY A 228 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG A 253 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU A 226 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 183 through 186 Processing sheet with id= E, first strand: chain 'A' and resid 137 through 142 removed outlier: 6.921A pdb=" N SER A 169 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER A 140 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR A 167 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.172A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.946A pdb=" N MET B 49 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.863A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.607A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 179 through 183 removed outlier: 6.153A pdb=" N THR C 51 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLN C 182 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE C 53 " --> pdb=" O GLN C 182 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 57 through 59 Processing sheet with id= L, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.571A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 116 through 121 removed outlier: 6.777A pdb=" N ASP C 148 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA C 119 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N THR C 146 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 164 through 168 removed outlier: 6.172A pdb=" N VAL D 36 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N TYR D 167 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL D 38 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.947A pdb=" N MET D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.862A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.608A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.173A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 49 through 51 removed outlier: 3.947A pdb=" N MET E 49 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.862A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.607A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'N' and resid 2 through 7 removed outlier: 3.550A pdb=" N THR N 465 " --> pdb=" O ASP N 460 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'N' and resid 506 through 508 removed outlier: 3.594A pdb=" N VAL N 508 " --> pdb=" O ALA N 479 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE N 420 " --> pdb=" O LYS N 486 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ARG N 425 " --> pdb=" O PHE N 434 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N PHE N 434 " --> pdb=" O ARG N 425 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'N' and resid 484 through 486 removed outlier: 3.892A pdb=" N TYR N 501 " --> pdb=" O ALA N 485 " (cutoff:3.500A) 678 hydrogen bonds defined for protein. 1957 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: 5.00 Time building geometry restraints manager: 6.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4447 1.34 - 1.46: 3884 1.46 - 1.58: 6678 1.58 - 1.69: 0 1.69 - 1.81: 155 Bond restraints: 15164 Sorted by residual: bond pdb=" CG ABU B 501 " pdb=" CD ABU B 501 " ideal model delta sigma weight residual 1.540 1.501 0.039 2.00e-02 2.50e+03 3.71e+00 bond pdb=" CG PRO C 159 " pdb=" CD PRO C 159 " ideal model delta sigma weight residual 1.512 1.490 0.022 2.70e-02 1.37e+03 6.74e-01 bond pdb=" CB VAL A 276 " pdb=" CG1 VAL A 276 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.18e-01 bond pdb=" C1 MAN a 5 " pdb=" O5 MAN a 5 " ideal model delta sigma weight residual 1.406 1.429 -0.023 3.40e-02 8.65e+02 4.41e-01 bond pdb=" C1 MAN G 5 " pdb=" O5 MAN G 5 " ideal model delta sigma weight residual 1.406 1.428 -0.022 3.40e-02 8.65e+02 4.38e-01 ... (remaining 15159 not shown) Histogram of bond angle deviations from ideal: 100.16 - 106.93: 450 106.93 - 113.69: 8525 113.69 - 120.46: 5600 120.46 - 127.23: 5882 127.23 - 134.00: 162 Bond angle restraints: 20619 Sorted by residual: angle pdb=" CG ABU B 501 " pdb=" CD ABU B 501 " pdb=" OE2 ABU B 501 " ideal model delta sigma weight residual 115.90 123.15 -7.25 3.00e+00 1.11e-01 5.84e+00 angle pdb=" C MET A 145 " pdb=" N THR A 146 " pdb=" CA THR A 146 " ideal model delta sigma weight residual 121.54 125.93 -4.39 1.91e+00 2.74e-01 5.27e+00 angle pdb=" C3 MAN H 4 " pdb=" C2 MAN H 4 " pdb=" O2 MAN H 4 " ideal model delta sigma weight residual 105.65 110.01 -4.36 2.47e+00 1.64e-01 3.13e+00 angle pdb=" C3 MAN F 4 " pdb=" C2 MAN F 4 " pdb=" O2 MAN F 4 " ideal model delta sigma weight residual 105.65 110.00 -4.35 2.47e+00 1.64e-01 3.11e+00 angle pdb=" C3 MAN a 5 " pdb=" C2 MAN a 5 " pdb=" O2 MAN a 5 " ideal model delta sigma weight residual 105.65 109.99 -4.34 2.47e+00 1.64e-01 3.10e+00 ... (remaining 20614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 8585 17.38 - 34.76: 252 34.76 - 52.14: 34 52.14 - 69.51: 13 69.51 - 86.89: 5 Dihedral angle restraints: 8889 sinusoidal: 3673 harmonic: 5216 Sorted by residual: dihedral pdb=" N ASP B 424 " pdb=" CA ASP B 424 " pdb=" CB ASP B 424 " pdb=" CG ASP B 424 " ideal model delta sinusoidal sigma weight residual -60.00 -118.79 58.79 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N ASP D 424 " pdb=" CA ASP D 424 " pdb=" CB ASP D 424 " pdb=" CG ASP D 424 " ideal model delta sinusoidal sigma weight residual -60.00 -118.74 58.74 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N ASP E 424 " pdb=" CA ASP E 424 " pdb=" CB ASP E 424 " pdb=" CG ASP E 424 " ideal model delta sinusoidal sigma weight residual -60.00 -118.72 58.72 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 8886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2067 0.056 - 0.112: 303 0.112 - 0.168: 22 0.168 - 0.224: 5 0.224 - 0.280: 1 Chirality restraints: 2398 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.46e+01 chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.07e+01 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.36e+01 ... (remaining 2395 not shown) Planarity restraints: 2514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 302 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C VAL D 302 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL D 302 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN D 303 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 302 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C VAL B 302 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL B 302 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN B 303 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 302 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" C VAL E 302 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL E 302 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN E 303 " 0.009 2.00e-02 2.50e+03 ... (remaining 2511 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3595 2.80 - 3.32: 13722 3.32 - 3.85: 25247 3.85 - 4.37: 30470 4.37 - 4.90: 51639 Nonbonded interactions: 124673 Sorted by model distance: nonbonded pdb=" O VAL C 248 " pdb=" OG SER C 251 " model vdw 2.271 2.440 nonbonded pdb=" OG SER C 286 " pdb=" NZ LYS D 274 " model vdw 2.273 2.520 nonbonded pdb=" ND2 ASN D 243 " pdb=" OD2 ASP D 245 " model vdw 2.274 2.520 nonbonded pdb=" ND2 ASN B 243 " pdb=" OD2 ASP B 245 " model vdw 2.275 2.520 nonbonded pdb=" ND2 ASN E 243 " pdb=" OD2 ASP E 245 " model vdw 2.275 2.520 ... (remaining 124668 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 'B' and (resid 7 through 43 or resid 45 through 65 or resid 67 through 44 \ 7)) selection = (chain 'D' and (resid 7 through 43 or resid 45 through 65 or resid 67 through 44 \ 7)) selection = (chain 'E' and (resid 7 through 43 or resid 45 through 65 or resid 67 through 44 \ 7)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'a' } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'e' } 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: 4 Type Number sf(0) Gaussians S 89 5.16 5 C 9626 2.51 5 N 2362 2.21 5 O 2700 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 6.770 Check model and map are aligned: 0.250 Process input model: 44.350 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 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 : 0.002 0.039 15164 Z= 0.158 Angle : 0.420 7.250 20619 Z= 0.210 Chirality : 0.041 0.280 2398 Planarity : 0.003 0.029 2505 Dihedral : 9.013 86.893 5527 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.88 (0.21), residues: 1744 helix: 2.04 (0.22), residues: 560 sheet: 1.15 (0.24), residues: 479 loop : 0.81 (0.25), residues: 705 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 364 time to evaluate : 1.855 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: 12 outliers final: 2 residues processed: 371 average time/residue: 1.3842 time to fit residues: 559.8251 Evaluate side-chains 208 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 206 time to evaluate : 1.781 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 1.2191 time to fit residues: 3.6969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.0970 chunk 131 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 0.1980 chunk 100 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 overall best weight: 1.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 345 ASN A 347 GLN C 54 HIS C 80 GLN C 154 GLN C 156 HIS ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 15164 Z= 0.240 Angle : 0.627 9.139 20619 Z= 0.327 Chirality : 0.044 0.384 2398 Planarity : 0.004 0.060 2505 Dihedral : 4.732 59.808 2196 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 3.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.79 (0.21), residues: 1744 helix: 2.15 (0.21), residues: 565 sheet: 0.93 (0.24), residues: 451 loop : 0.72 (0.25), residues: 728 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 234 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 15 residues processed: 254 average time/residue: 1.3861 time to fit residues: 384.8546 Evaluate side-chains 212 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 197 time to evaluate : 1.821 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 0.3763 time to fit residues: 5.4461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 130 optimal weight: 0.3980 chunk 106 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 15164 Z= 0.333 Angle : 0.661 12.599 20619 Z= 0.341 Chirality : 0.045 0.271 2398 Planarity : 0.004 0.060 2505 Dihedral : 4.888 54.446 2196 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.36 (0.21), residues: 1744 helix: 1.79 (0.22), residues: 576 sheet: 0.60 (0.24), residues: 467 loop : 0.51 (0.25), residues: 701 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 214 time to evaluate : 1.952 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: 42 outliers final: 18 residues processed: 231 average time/residue: 1.4219 time to fit residues: 358.9072 Evaluate side-chains 195 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 1.852 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 10 residues processed: 8 average time/residue: 0.3161 time to fit residues: 5.8307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 17 optimal weight: 0.0670 chunk 75 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 167 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 15164 Z= 0.226 Angle : 0.603 9.820 20619 Z= 0.309 Chirality : 0.043 0.252 2398 Planarity : 0.004 0.035 2505 Dihedral : 4.748 50.372 2196 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.36 (0.21), residues: 1744 helix: 1.96 (0.22), residues: 570 sheet: 0.71 (0.24), residues: 447 loop : 0.29 (0.25), residues: 727 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 181 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 19 residues processed: 198 average time/residue: 1.3301 time to fit residues: 290.4875 Evaluate side-chains 190 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 1.773 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 10 residues processed: 9 average time/residue: 0.7465 time to fit residues: 10.0488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 42 optimal weight: 0.0870 overall best weight: 2.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN D 267 HIS ** N 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 507 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 15164 Z= 0.331 Angle : 0.629 10.190 20619 Z= 0.326 Chirality : 0.045 0.236 2398 Planarity : 0.004 0.031 2505 Dihedral : 4.845 43.860 2196 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 2.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.08 (0.21), residues: 1744 helix: 1.83 (0.22), residues: 573 sheet: 0.31 (0.24), residues: 464 loop : 0.21 (0.24), residues: 707 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 176 time to evaluate : 1.723 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: 46 outliers final: 20 residues processed: 200 average time/residue: 1.3129 time to fit residues: 289.2812 Evaluate side-chains 178 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 158 time to evaluate : 1.632 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 6 average time/residue: 0.6853 time to fit residues: 7.1382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 0.0060 chunk 150 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN C 154 GLN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 15164 Z= 0.211 Angle : 0.591 11.120 20619 Z= 0.300 Chirality : 0.043 0.247 2398 Planarity : 0.003 0.034 2505 Dihedral : 4.701 42.250 2196 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.21 (0.21), residues: 1744 helix: 1.98 (0.22), residues: 570 sheet: 0.42 (0.24), residues: 450 loop : 0.21 (0.24), residues: 724 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 166 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 22 residues processed: 187 average time/residue: 1.4172 time to fit residues: 290.1202 Evaluate side-chains 179 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 157 time to evaluate : 1.814 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 16 residues processed: 6 average time/residue: 0.6905 time to fit residues: 7.1362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 166 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 15164 Z= 0.208 Angle : 0.595 11.771 20619 Z= 0.301 Chirality : 0.042 0.240 2398 Planarity : 0.003 0.033 2505 Dihedral : 4.608 43.928 2196 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.21 (0.21), residues: 1744 helix: 2.02 (0.22), residues: 569 sheet: 0.41 (0.24), residues: 455 loop : 0.19 (0.25), residues: 720 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 160 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 18 residues processed: 181 average time/residue: 1.3658 time to fit residues: 273.4925 Evaluate side-chains 175 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 1.912 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.4878 time to fit residues: 4.9917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 131 optimal weight: 0.0770 chunk 151 optimal weight: 0.7980 overall best weight: 1.2740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 15164 Z= 0.212 Angle : 0.604 11.595 20619 Z= 0.307 Chirality : 0.042 0.232 2398 Planarity : 0.003 0.031 2505 Dihedral : 4.589 45.424 2196 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.21 (0.21), residues: 1744 helix: 2.02 (0.22), residues: 565 sheet: 0.52 (0.25), residues: 446 loop : 0.12 (0.24), residues: 733 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 181 average time/residue: 1.3878 time to fit residues: 276.8031 Evaluate side-chains 173 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 1.812 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.7026 time to fit residues: 5.6980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 155 optimal weight: 0.0870 chunk 93 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 15164 Z= 0.240 Angle : 0.626 14.544 20619 Z= 0.316 Chirality : 0.043 0.230 2398 Planarity : 0.003 0.030 2505 Dihedral : 4.599 46.872 2196 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.14 (0.21), residues: 1744 helix: 1.99 (0.22), residues: 565 sheet: 0.44 (0.24), residues: 453 loop : 0.09 (0.24), residues: 726 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 182 average time/residue: 1.3540 time to fit residues: 271.4444 Evaluate side-chains 175 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 1.760 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.7111 time to fit residues: 3.9822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 0.0020 chunk 100 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 158 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 15164 Z= 0.215 Angle : 0.642 14.258 20619 Z= 0.320 Chirality : 0.043 0.206 2398 Planarity : 0.003 0.032 2505 Dihedral : 4.603 48.117 2196 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.15 (0.21), residues: 1744 helix: 1.99 (0.22), residues: 565 sheet: 0.41 (0.24), residues: 480 loop : 0.11 (0.25), residues: 699 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 179 average time/residue: 1.3971 time to fit residues: 277.2649 Evaluate side-chains 173 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 1.798 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 0.2967 time to fit residues: 2.6657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 504 GLN ** 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 = 0.3353 r_free = 0.3353 target = 0.081732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.059607 restraints weight = 56404.974| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 4.08 r_work: 0.2690 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 15164 Z= 0.186 Angle : 0.628 13.009 20619 Z= 0.313 Chirality : 0.042 0.242 2398 Planarity : 0.003 0.034 2505 Dihedral : 4.540 49.647 2196 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.24 % 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: 1.22 (0.21), residues: 1744 helix: 2.01 (0.22), residues: 566 sheet: 0.45 (0.24), residues: 475 loop : 0.19 (0.25), residues: 703 =============================================================================== Job complete usr+sys time: 5490.51 seconds wall clock time: 98 minutes 9.85 seconds (5889.85 seconds total)