Starting phenix.real_space_refine on Sat Mar 16 13:26:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qna_14072/03_2024/7qna_14072_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qna_14072/03_2024/7qna_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_14072/03_2024/7qna_14072.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qna_14072/03_2024/7qna_14072.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qna_14072/03_2024/7qna_14072_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qna_14072/03_2024/7qna_14072_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. Process input model Symmetric amino acids flipped Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 15 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 dihedrals: 6 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: 15 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 dihedrals: 6 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: 15 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 dihedrals: 6 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: 15 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 dihedrals: 3 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 dihedrals: 3 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: 11.85, per 1000 atoms: 0.80 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: 6.51 Conformation dependent library (CDL) restraints added in 4.4 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: 3.05 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: 5.19 Time building geometry restraints manager: 6.94 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=" C1 MAN a 5 " pdb=" O5 MAN a 5 " ideal model delta sigma weight residual 1.399 1.429 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 MAN G 5 " pdb=" O5 MAN G 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C1 MAN G 4 " pdb=" O5 MAN G 4 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 MAN F 5 " pdb=" O5 MAN F 5 " ideal model delta sigma weight residual 1.399 1.428 -0.029 2.00e-02 2.50e+03 2.08e+00 ... (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 BMA G 3 " pdb=" C2 BMA G 3 " pdb=" O2 BMA G 3 " ideal model delta sigma weight residual 112.95 106.60 6.35 3.00e+00 1.11e-01 4.48e+00 angle pdb=" C3 BMA H 3 " pdb=" C2 BMA H 3 " pdb=" O2 BMA H 3 " ideal model delta sigma weight residual 112.95 106.61 6.34 3.00e+00 1.11e-01 4.47e+00 angle pdb=" C3 BMA a 3 " pdb=" C2 BMA a 3 " pdb=" O2 BMA a 3 " ideal model delta sigma weight residual 112.95 106.65 6.30 3.00e+00 1.11e-01 4.41e+00 ... (remaining 20614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 8992 21.64 - 43.27: 179 43.27 - 64.91: 20 64.91 - 86.55: 27 86.55 - 108.19: 19 Dihedral angle restraints: 9237 sinusoidal: 4021 harmonic: 5216 Sorted by residual: dihedral pdb=" O4 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.48 108.19 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" O4 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C5 BMA a 3 " pdb=" O5 BMA a 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.24 107.95 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" O4 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.67 107.38 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 9234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2064 0.057 - 0.115: 304 0.115 - 0.172: 20 0.172 - 0.230: 5 0.230 - 0.287: 5 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 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: 1.700 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: 5.970 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 49.270 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 : 0.003 0.039 15164 Z= 0.196 Angle : 0.484 7.250 20619 Z= 0.222 Chirality : 0.043 0.287 2398 Planarity : 0.003 0.029 2505 Dihedral : 11.462 108.185 5875 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 % Allowed : 3.02 % Favored : 96.22 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 443 HIS 0.002 0.001 HIS D 267 PHE 0.006 0.001 PHE A 190 TYR 0.010 0.001 TYR E 299 ARG 0.003 0.000 ARG B 196 *********************** 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 : 1.807 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: A 48 PHE cc_start: 0.8104 (m-80) cc_final: 0.7886 (m-80) REVERT: A 345 ASN cc_start: 0.7226 (m110) cc_final: 0.7005 (m-40) REVERT: B 9 MET cc_start: 0.7537 (mtp) cc_final: 0.7163 (ttm) REVERT: B 90 GLN cc_start: 0.8386 (mp10) cc_final: 0.7879 (mp10) REVERT: C 152 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7907 (mm-40) REVERT: C 162 GLU cc_start: 0.8399 (tt0) cc_final: 0.8180 (tm-30) REVERT: D 55 MET cc_start: 0.8733 (mtt) cc_final: 0.8112 (mmm) REVERT: D 85 ASN cc_start: 0.8671 (p0) cc_final: 0.8362 (p0) REVERT: D 90 GLN cc_start: 0.8289 (mp10) cc_final: 0.8040 (pm20) REVERT: D 147 GLU cc_start: 0.7526 (tt0) cc_final: 0.7144 (tt0) REVERT: D 230 ILE cc_start: 0.9379 (mt) cc_final: 0.9001 (mp) REVERT: D 234 ILE cc_start: 0.9340 (mt) cc_final: 0.9098 (mp) REVERT: E 31 PHE cc_start: 0.8546 (t80) cc_final: 0.8267 (t80) REVERT: E 155 GLU cc_start: 0.7941 (tt0) cc_final: 0.7536 (tt0) REVERT: E 298 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8671 (tm-30) REVERT: N 4 LEU cc_start: 0.8911 (mt) cc_final: 0.8696 (mt) REVERT: N 407 LEU cc_start: 0.7966 (mp) cc_final: 0.7685 (mp) REVERT: N 426 GLN cc_start: 0.7856 (tt0) cc_final: 0.7579 (tt0) REVERT: N 452 LYS cc_start: 0.8718 (ttmt) cc_final: 0.8512 (tppp) REVERT: N 454 ARG cc_start: 0.6827 (mtm110) cc_final: 0.6424 (mtp-110) REVERT: N 472 ASN cc_start: 0.8266 (t0) cc_final: 0.7592 (t0) REVERT: N 480 VAL cc_start: 0.8698 (t) cc_final: 0.8216 (p) outliers start: 12 outliers final: 2 residues processed: 371 average time/residue: 1.3538 time to fit residues: 547.9463 Evaluate side-chains 213 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 211 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain B residue 36 VAL 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: 5.9990 chunk 72 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 88 optimal weight: 0.0370 chunk 70 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 overall best weight: 2.2262 ------------------------------------------------------------------------------- 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: 0.8547 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 15164 Z= 0.316 Angle : 0.649 8.895 20619 Z= 0.335 Chirality : 0.045 0.334 2398 Planarity : 0.004 0.054 2505 Dihedral : 9.385 80.551 2548 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.21 % Allowed : 14.37 % Favored : 82.42 % 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: 1.75 (0.21), residues: 1744 helix: 2.15 (0.22), residues: 565 sheet: 0.91 (0.24), residues: 451 loop : 0.68 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 241 HIS 0.003 0.001 HIS A 184 PHE 0.015 0.002 PHE B 31 TYR 0.024 0.002 TYR D 299 ARG 0.009 0.001 ARG C 185 *********************** 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 298 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 247 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8030 (mpp) cc_final: 0.7773 (mmt) REVERT: A 253 ARG cc_start: 0.7990 (tpp-160) cc_final: 0.7289 (mmp-170) REVERT: B 9 MET cc_start: 0.7472 (mtp) cc_final: 0.6951 (ttm) REVERT: B 90 GLN cc_start: 0.8446 (mp10) cc_final: 0.7974 (mp10) REVERT: C 209 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8684 (p) REVERT: D 13 LYS cc_start: 0.8755 (tmmt) cc_final: 0.8334 (tmmt) REVERT: D 14 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8543 (mp0) REVERT: D 55 MET cc_start: 0.8855 (mtt) cc_final: 0.8421 (mmm) REVERT: D 147 GLU cc_start: 0.7791 (tt0) cc_final: 0.7370 (tm-30) REVERT: D 224 GLN cc_start: 0.7926 (tp40) cc_final: 0.7692 (tp40) REVERT: D 230 ILE cc_start: 0.9433 (mt) cc_final: 0.8985 (mp) REVERT: E 90 GLN cc_start: 0.8720 (mp10) cc_final: 0.8352 (pm20) REVERT: E 298 GLU cc_start: 0.9314 (tm-30) cc_final: 0.9090 (tm-30) REVERT: N 421 MET cc_start: 0.8169 (tpp) cc_final: 0.7850 (mpp) REVERT: N 425 ARG cc_start: 0.8339 (ptt180) cc_final: 0.7953 (ptt-90) REVERT: N 433 GLU cc_start: 0.8941 (tp30) cc_final: 0.8618 (mp0) REVERT: N 452 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8489 (tppp) REVERT: N 454 ARG cc_start: 0.6758 (mtm110) cc_final: 0.6527 (mtp-110) REVERT: N 472 ASN cc_start: 0.8230 (t0) cc_final: 0.7704 (t0) REVERT: N 480 VAL cc_start: 0.8795 (t) cc_final: 0.8329 (p) outliers start: 51 outliers final: 14 residues processed: 269 average time/residue: 1.3845 time to fit residues: 406.5923 Evaluate side-chains 196 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 181 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain N residue 477 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 157 optimal weight: 0.6980 chunk 170 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15164 Z= 0.199 Angle : 0.611 9.286 20619 Z= 0.313 Chirality : 0.044 0.204 2398 Planarity : 0.004 0.099 2505 Dihedral : 8.312 71.806 2544 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.33 % Allowed : 16.19 % Favored : 81.47 % 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: 1.68 (0.21), residues: 1744 helix: 2.11 (0.22), residues: 563 sheet: 0.90 (0.25), residues: 445 loop : 0.60 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 241 HIS 0.006 0.001 HIS A 184 PHE 0.024 0.001 PHE C 417 TYR 0.022 0.001 TYR D 299 ARG 0.007 0.000 ARG D 86 *********************** 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 232 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 195 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8040 (mpp) cc_final: 0.7784 (mmt) REVERT: B 9 MET cc_start: 0.7027 (mtp) cc_final: 0.6642 (ttm) REVERT: B 90 GLN cc_start: 0.8434 (mp10) cc_final: 0.7944 (mp10) REVERT: C 71 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7763 (mm-30) REVERT: C 168 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: D 55 MET cc_start: 0.8854 (mtt) cc_final: 0.8434 (mmm) REVERT: D 61 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8258 (ptp) REVERT: D 185 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: E 9 MET cc_start: 0.7814 (mmt) cc_final: 0.7443 (mpt) REVERT: E 90 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: E 155 GLU cc_start: 0.8098 (tt0) cc_final: 0.7490 (mt-10) REVERT: E 190 GLU cc_start: 0.8181 (tt0) cc_final: 0.7946 (tt0) REVERT: E 298 GLU cc_start: 0.9318 (tm-30) cc_final: 0.9090 (tm-30) REVERT: N 425 ARG cc_start: 0.8346 (ptt180) cc_final: 0.7965 (ptt-90) REVERT: N 433 GLU cc_start: 0.8921 (tp30) cc_final: 0.8597 (mp0) REVERT: N 452 LYS cc_start: 0.8744 (ttmt) cc_final: 0.8477 (tppp) REVERT: N 454 ARG cc_start: 0.6744 (mtm110) cc_final: 0.6482 (mtp-110) REVERT: N 463 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.9044 (tppp) REVERT: N 472 ASN cc_start: 0.8166 (t0) cc_final: 0.7543 (t0) REVERT: N 480 VAL cc_start: 0.8799 (t) cc_final: 0.8272 (p) REVERT: N 482 TYR cc_start: 0.8231 (m-80) cc_final: 0.7882 (m-80) REVERT: N 504 GLN cc_start: 0.8639 (mp10) cc_final: 0.8407 (pm20) outliers start: 37 outliers final: 13 residues processed: 213 average time/residue: 1.3259 time to fit residues: 310.8121 Evaluate side-chains 199 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 181 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain N residue 463 LYS Chi-restraints excluded: chain N residue 477 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 5.9990 chunk 118 optimal weight: 0.0970 chunk 81 optimal weight: 9.9990 chunk 17 optimal weight: 0.0770 chunk 75 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3302 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= 0.176 Angle : 0.584 8.188 20619 Z= 0.294 Chirality : 0.043 0.229 2398 Planarity : 0.003 0.036 2505 Dihedral : 7.413 65.851 2544 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.14 % Allowed : 17.14 % Favored : 80.72 % 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: 1.63 (0.21), residues: 1744 helix: 2.20 (0.22), residues: 560 sheet: 0.91 (0.25), residues: 442 loop : 0.42 (0.25), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 241 HIS 0.003 0.001 HIS A 184 PHE 0.013 0.001 PHE A 48 TYR 0.023 0.001 TYR E 299 ARG 0.007 0.000 ARG E 180 *********************** 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 219 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 185 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8138 (mpp) cc_final: 0.7834 (mmt) REVERT: A 253 ARG cc_start: 0.7982 (tpp-160) cc_final: 0.7781 (mmt180) REVERT: B 9 MET cc_start: 0.6919 (mtp) cc_final: 0.6647 (ttm) REVERT: B 90 GLN cc_start: 0.8427 (mp10) cc_final: 0.7923 (mp10) REVERT: C 168 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: D 55 MET cc_start: 0.8878 (mtt) cc_final: 0.8473 (mmm) REVERT: D 185 GLN cc_start: 0.8207 (mp10) cc_final: 0.7811 (pm20) REVERT: D 224 GLN cc_start: 0.7892 (tp40) cc_final: 0.7474 (tp40) REVERT: E 9 MET cc_start: 0.7731 (mmt) cc_final: 0.7509 (mmt) REVERT: E 90 GLN cc_start: 0.8803 (mp10) cc_final: 0.8336 (pm20) REVERT: E 155 GLU cc_start: 0.8060 (tt0) cc_final: 0.7544 (mt-10) REVERT: E 181 ILE cc_start: 0.9188 (mm) cc_final: 0.8956 (mm) REVERT: E 190 GLU cc_start: 0.8175 (tt0) cc_final: 0.7939 (tt0) REVERT: N 425 ARG cc_start: 0.8385 (ptt180) cc_final: 0.8000 (ptt-90) REVERT: N 433 GLU cc_start: 0.8895 (tp30) cc_final: 0.8643 (mp0) REVERT: N 454 ARG cc_start: 0.6779 (mtm110) cc_final: 0.6527 (mtp-110) REVERT: N 463 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9128 (tppp) REVERT: N 472 ASN cc_start: 0.8038 (t0) cc_final: 0.7501 (t0) REVERT: N 480 VAL cc_start: 0.8835 (t) cc_final: 0.8383 (p) REVERT: N 482 TYR cc_start: 0.8228 (m-80) cc_final: 0.8011 (m-80) outliers start: 34 outliers final: 16 residues processed: 201 average time/residue: 1.3534 time to fit residues: 298.4656 Evaluate side-chains 194 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 176 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain N residue 407 LEU Chi-restraints excluded: chain N residue 463 LYS Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain N residue 477 ASP 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: 6.9990 chunk 2 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 42 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: ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN N 426 GLN N 507 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 15164 Z= 0.455 Angle : 0.717 11.945 20619 Z= 0.367 Chirality : 0.048 0.236 2398 Planarity : 0.005 0.077 2505 Dihedral : 7.250 65.313 2544 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.15 % Allowed : 16.19 % Favored : 80.66 % 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: 1.00 (0.21), residues: 1744 helix: 1.67 (0.22), residues: 577 sheet: 0.43 (0.24), residues: 453 loop : 0.11 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 241 HIS 0.006 0.002 HIS C 318 PHE 0.029 0.002 PHE C 417 TYR 0.033 0.002 TYR D 299 ARG 0.013 0.001 ARG D 26 *********************** 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 226 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 176 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8064 (mpp) cc_final: 0.7808 (mmt) REVERT: A 262 GLN cc_start: 0.8916 (tp40) cc_final: 0.8712 (tp40) REVERT: A 272 ILE cc_start: 0.9584 (OUTLIER) cc_final: 0.9365 (mp) REVERT: C 102 MET cc_start: 0.8155 (tpp) cc_final: 0.7936 (tpp) REVERT: C 105 LYS cc_start: 0.9114 (mmtt) cc_final: 0.8772 (mppt) REVERT: C 168 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: C 189 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7371 (tm-30) REVERT: C 199 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7684 (p90) REVERT: D 55 MET cc_start: 0.9030 (mtt) cc_final: 0.8734 (mmm) REVERT: D 185 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7988 (pm20) REVERT: E 9 MET cc_start: 0.7733 (mmt) cc_final: 0.7392 (mpt) REVERT: E 90 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8516 (pm20) REVERT: E 137 MET cc_start: 0.8562 (mmm) cc_final: 0.8316 (tpp) REVERT: N 425 ARG cc_start: 0.8683 (ptt180) cc_final: 0.8222 (ptt-90) REVERT: N 433 GLU cc_start: 0.8937 (tp30) cc_final: 0.8698 (mp0) REVERT: N 452 LYS cc_start: 0.8530 (tppp) cc_final: 0.8304 (tppp) REVERT: N 454 ARG cc_start: 0.6889 (mtm110) cc_final: 0.6622 (mtp-110) REVERT: N 472 ASN cc_start: 0.8272 (t0) cc_final: 0.7882 (t0) REVERT: N 480 VAL cc_start: 0.8987 (t) cc_final: 0.8445 (p) REVERT: N 482 TYR cc_start: 0.8228 (m-80) cc_final: 0.7822 (m-80) REVERT: N 504 GLN cc_start: 0.8602 (mp10) cc_final: 0.8389 (pm20) outliers start: 50 outliers final: 26 residues processed: 205 average time/residue: 1.2352 time to fit residues: 279.9713 Evaluate side-chains 194 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 407 LEU Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain N residue 477 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 167 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15164 Z= 0.172 Angle : 0.587 9.197 20619 Z= 0.297 Chirality : 0.043 0.239 2398 Planarity : 0.003 0.036 2505 Dihedral : 6.521 57.505 2544 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.14 % Allowed : 18.15 % Favored : 79.71 % 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: 1.25 (0.21), residues: 1744 helix: 2.01 (0.22), residues: 573 sheet: 0.53 (0.24), residues: 434 loop : 0.17 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 241 HIS 0.004 0.001 HIS B 267 PHE 0.013 0.001 PHE C 308 TYR 0.024 0.001 TYR E 299 ARG 0.006 0.000 ARG A 118 *********************** 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 216 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 182 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8050 (mpp) cc_final: 0.7772 (mmt) REVERT: A 181 MET cc_start: 0.9028 (mtm) cc_final: 0.8705 (pmm) REVERT: A 189 LYS cc_start: 0.9009 (mttt) cc_final: 0.8719 (mttp) REVERT: A 253 ARG cc_start: 0.7988 (mmt180) cc_final: 0.7383 (mmp-170) REVERT: A 262 GLN cc_start: 0.8838 (tp40) cc_final: 0.8623 (tp40) REVERT: C 71 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7642 (mm-30) REVERT: C 105 LYS cc_start: 0.9099 (mmtt) cc_final: 0.8848 (mppt) REVERT: C 189 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7543 (tm-30) REVERT: D 13 LYS cc_start: 0.8870 (tmmt) cc_final: 0.8618 (tmmt) REVERT: D 18 LYS cc_start: 0.9345 (pttp) cc_final: 0.9110 (pptt) REVERT: D 185 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.8042 (pm20) REVERT: D 224 GLN cc_start: 0.8010 (tp40) cc_final: 0.7676 (tp40) REVERT: E 9 MET cc_start: 0.7777 (mmt) cc_final: 0.7407 (mpt) REVERT: E 90 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8294 (pm20) REVERT: E 180 ARG cc_start: 0.8016 (mmp80) cc_final: 0.7811 (mtm180) REVERT: N 425 ARG cc_start: 0.8654 (ptt180) cc_final: 0.8160 (ptt-90) REVERT: N 433 GLU cc_start: 0.8916 (tp30) cc_final: 0.8713 (mp0) REVERT: N 452 LYS cc_start: 0.8546 (tppp) cc_final: 0.8323 (tppp) REVERT: N 454 ARG cc_start: 0.6916 (mtm110) cc_final: 0.6609 (mtp-110) REVERT: N 472 ASN cc_start: 0.8295 (t0) cc_final: 0.7849 (t0) REVERT: N 480 VAL cc_start: 0.8936 (t) cc_final: 0.8376 (p) REVERT: N 482 TYR cc_start: 0.8210 (m-80) cc_final: 0.7820 (m-80) REVERT: N 504 GLN cc_start: 0.8573 (mp10) cc_final: 0.8303 (pm20) outliers start: 34 outliers final: 18 residues processed: 200 average time/residue: 1.3751 time to fit residues: 301.5219 Evaluate side-chains 188 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain N residue 477 ASP 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: 0.2980 chunk 95 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 166 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 15164 Z= 0.193 Angle : 0.592 11.834 20619 Z= 0.295 Chirality : 0.043 0.241 2398 Planarity : 0.003 0.035 2505 Dihedral : 6.075 52.586 2544 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.14 % Allowed : 18.02 % Favored : 79.84 % 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: 1.29 (0.21), residues: 1744 helix: 2.06 (0.22), residues: 572 sheet: 0.60 (0.25), residues: 434 loop : 0.16 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP E 241 HIS 0.002 0.001 HIS D 267 PHE 0.028 0.001 PHE C 417 TYR 0.025 0.001 TYR D 299 ARG 0.007 0.000 ARG C 185 *********************** 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 206 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 172 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7799 (mmt) REVERT: A 189 LYS cc_start: 0.9005 (mttt) cc_final: 0.8655 (mtmm) REVERT: A 253 ARG cc_start: 0.7992 (mmt180) cc_final: 0.7432 (mmp-170) REVERT: B 55 MET cc_start: 0.8764 (mtm) cc_final: 0.8213 (mmm) REVERT: B 137 MET cc_start: 0.7229 (mmm) cc_final: 0.6648 (ttm) REVERT: C 71 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7647 (mp0) REVERT: C 105 LYS cc_start: 0.9133 (mmtt) cc_final: 0.8915 (mppt) REVERT: C 189 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7560 (tm-30) REVERT: D 185 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8037 (pm20) REVERT: D 224 GLN cc_start: 0.8048 (tp40) cc_final: 0.7689 (tp40) REVERT: E 9 MET cc_start: 0.7776 (mmt) cc_final: 0.7552 (mmt) REVERT: E 90 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8313 (pm20) REVERT: E 282 ASP cc_start: 0.8245 (m-30) cc_final: 0.7884 (m-30) REVERT: N 421 MET cc_start: 0.8306 (tpp) cc_final: 0.7852 (mpp) REVERT: N 425 ARG cc_start: 0.8616 (ptt180) cc_final: 0.8084 (ptt-90) REVERT: N 433 GLU cc_start: 0.8906 (tp30) cc_final: 0.8703 (mp0) REVERT: N 452 LYS cc_start: 0.8536 (tppp) cc_final: 0.8300 (tppp) REVERT: N 454 ARG cc_start: 0.6919 (mtm110) cc_final: 0.6633 (mtp-110) REVERT: N 472 ASN cc_start: 0.8273 (t0) cc_final: 0.7863 (t0) REVERT: N 480 VAL cc_start: 0.8934 (t) cc_final: 0.8375 (p) REVERT: N 482 TYR cc_start: 0.8197 (m-80) cc_final: 0.7813 (m-80) outliers start: 34 outliers final: 18 residues processed: 191 average time/residue: 1.2950 time to fit residues: 272.3193 Evaluate side-chains 187 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain N residue 440 TRP Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain N residue 477 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 4.9990 chunk 66 optimal weight: 0.0570 chunk 99 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 151 optimal weight: 0.6980 overall best weight: 1.5502 ------------------------------------------------------------------------------- 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 239 GLN ** 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 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15164 Z= 0.234 Angle : 0.604 10.654 20619 Z= 0.305 Chirality : 0.044 0.239 2398 Planarity : 0.003 0.031 2505 Dihedral : 5.823 48.993 2544 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.08 % Allowed : 18.40 % Favored : 79.52 % 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: 1.24 (0.21), residues: 1744 helix: 2.04 (0.22), residues: 568 sheet: 0.60 (0.24), residues: 446 loop : 0.08 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP D 241 HIS 0.003 0.001 HIS A 184 PHE 0.019 0.001 PHE A 337 TYR 0.028 0.001 TYR D 299 ARG 0.004 0.000 ARG N 459 *********************** 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 202 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7748 (mmt) REVERT: A 189 LYS cc_start: 0.9021 (mttt) cc_final: 0.8676 (mtmm) REVERT: B 55 MET cc_start: 0.8887 (mtm) cc_final: 0.8415 (mmm) REVERT: B 137 MET cc_start: 0.7436 (mmm) cc_final: 0.7168 (tpp) REVERT: C 71 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7561 (mp0) REVERT: C 102 MET cc_start: 0.8095 (tpp) cc_final: 0.7488 (tpp) REVERT: C 105 LYS cc_start: 0.9123 (mmtt) cc_final: 0.8837 (mppt) REVERT: C 189 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7512 (tm-30) REVERT: D 185 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8043 (pm20) REVERT: D 224 GLN cc_start: 0.8011 (tp40) cc_final: 0.7692 (tp40) REVERT: E 9 MET cc_start: 0.7838 (mmt) cc_final: 0.7577 (mmt) REVERT: E 90 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8333 (pm20) REVERT: N 421 MET cc_start: 0.8382 (tpp) cc_final: 0.7882 (mpp) REVERT: N 425 ARG cc_start: 0.8664 (ptt180) cc_final: 0.8148 (ptt-90) REVERT: N 452 LYS cc_start: 0.8529 (tppp) cc_final: 0.8297 (tppp) REVERT: N 454 ARG cc_start: 0.6927 (mtm110) cc_final: 0.6603 (mtp-110) REVERT: N 472 ASN cc_start: 0.8279 (t0) cc_final: 0.7923 (t0) REVERT: N 480 VAL cc_start: 0.8989 (t) cc_final: 0.8457 (p) REVERT: N 482 TYR cc_start: 0.8208 (m-80) cc_final: 0.7823 (m-80) REVERT: N 504 GLN cc_start: 0.8605 (mp10) cc_final: 0.8398 (pm20) outliers start: 33 outliers final: 21 residues processed: 188 average time/residue: 1.2686 time to fit residues: 263.4796 Evaluate side-chains 186 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain N residue 440 TRP Chi-restraints excluded: chain N residue 464 ASN Chi-restraints excluded: chain N residue 477 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15164 Z= 0.312 Angle : 0.638 12.491 20619 Z= 0.320 Chirality : 0.045 0.239 2398 Planarity : 0.003 0.034 2505 Dihedral : 5.788 46.791 2544 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.89 % Allowed : 18.59 % Favored : 79.52 % 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: 1.12 (0.21), residues: 1744 helix: 1.95 (0.22), residues: 572 sheet: 0.52 (0.24), residues: 446 loop : -0.01 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP E 241 HIS 0.004 0.001 HIS A 143 PHE 0.034 0.002 PHE C 417 TYR 0.030 0.002 TYR D 299 ARG 0.004 0.000 ARG N 459 *********************** 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 194 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7750 (mmt) REVERT: A 181 MET cc_start: 0.8924 (mtm) cc_final: 0.8666 (pmm) REVERT: A 189 LYS cc_start: 0.9052 (mttt) cc_final: 0.8708 (mtmm) REVERT: B 137 MET cc_start: 0.7543 (mmm) cc_final: 0.7324 (tpp) REVERT: C 102 MET cc_start: 0.8114 (tpp) cc_final: 0.7465 (tpp) REVERT: C 105 LYS cc_start: 0.9121 (mmtt) cc_final: 0.8815 (mppt) REVERT: C 189 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7427 (tm-30) REVERT: D 185 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8048 (pm20) REVERT: D 224 GLN cc_start: 0.7933 (tp40) cc_final: 0.7545 (tp40) REVERT: E 9 MET cc_start: 0.7814 (mmt) cc_final: 0.7519 (mmt) REVERT: E 90 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8328 (pm20) REVERT: N 421 MET cc_start: 0.8445 (tpp) cc_final: 0.7886 (mpp) REVERT: N 452 LYS cc_start: 0.8597 (tppp) cc_final: 0.8322 (tppp) REVERT: N 454 ARG cc_start: 0.6963 (mtm110) cc_final: 0.6680 (mtp-110) REVERT: N 469 GLU cc_start: 0.8420 (mp0) cc_final: 0.8148 (mm-30) REVERT: N 472 ASN cc_start: 0.8362 (t0) cc_final: 0.7975 (t0) REVERT: N 480 VAL cc_start: 0.9088 (t) cc_final: 0.8615 (p) REVERT: N 482 TYR cc_start: 0.8144 (m-80) cc_final: 0.7784 (m-80) REVERT: N 504 GLN cc_start: 0.8574 (mp10) cc_final: 0.8272 (pm20) outliers start: 30 outliers final: 19 residues processed: 181 average time/residue: 1.3259 time to fit residues: 264.5023 Evaluate side-chains 181 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain N residue 440 TRP Chi-restraints excluded: chain N residue 464 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 0.9990 chunk 100 optimal weight: 0.0170 chunk 77 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 172 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- 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 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.4860 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= 0.175 Angle : 0.597 12.442 20619 Z= 0.297 Chirality : 0.043 0.237 2398 Planarity : 0.003 0.034 2505 Dihedral : 5.454 42.264 2544 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.45 % Allowed : 19.28 % Favored : 79.27 % 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: 2.00 (0.22), residues: 568 sheet: 0.55 (0.24), residues: 473 loop : 0.11 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP E 241 HIS 0.002 0.001 HIS D 267 PHE 0.014 0.001 PHE C 308 TYR 0.024 0.001 TYR D 299 ARG 0.004 0.000 ARG N 459 ********************** 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 192 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 169 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7638 (mmt) REVERT: A 181 MET cc_start: 0.8911 (mtm) cc_final: 0.8637 (pmm) REVERT: A 189 LYS cc_start: 0.9018 (mttt) cc_final: 0.8677 (mtmm) REVERT: A 253 ARG cc_start: 0.8054 (mmt180) cc_final: 0.7541 (mmp-170) REVERT: A 348 MET cc_start: 0.6797 (ppp) cc_final: 0.5178 (mmp) REVERT: B 137 MET cc_start: 0.7456 (mmm) cc_final: 0.7116 (tpp) REVERT: C 71 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7572 (mp0) REVERT: C 189 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7479 (tm-30) REVERT: D 185 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: D 224 GLN cc_start: 0.7995 (tp40) cc_final: 0.7589 (tp40) REVERT: E 9 MET cc_start: 0.7772 (mmt) cc_final: 0.7503 (mmt) REVERT: E 90 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8371 (pm20) REVERT: N 421 MET cc_start: 0.8421 (tpp) cc_final: 0.8091 (mpp) REVERT: N 454 ARG cc_start: 0.7010 (mtm110) cc_final: 0.6540 (mtp-110) REVERT: N 469 GLU cc_start: 0.8445 (mp0) cc_final: 0.8163 (mm-30) REVERT: N 472 ASN cc_start: 0.8376 (t0) cc_final: 0.7879 (t0) REVERT: N 480 VAL cc_start: 0.9057 (t) cc_final: 0.8558 (p) REVERT: N 482 TYR cc_start: 0.8147 (m-80) cc_final: 0.7851 (m-80) REVERT: N 504 GLN cc_start: 0.8610 (mp10) cc_final: 0.8325 (pm20) outliers start: 23 outliers final: 17 residues processed: 183 average time/residue: 1.3384 time to fit residues: 269.4319 Evaluate side-chains 186 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain N residue 440 TRP Chi-restraints excluded: chain N residue 464 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 137 optimal weight: 0.0470 chunk 57 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.081668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.059715 restraints weight = 55744.070| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 4.05 r_work: 0.2688 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.4925 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= 0.175 Angle : 0.617 12.350 20619 Z= 0.302 Chirality : 0.043 0.230 2398 Planarity : 0.003 0.032 2505 Dihedral : 5.249 39.207 2544 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.32 % Allowed : 19.85 % Favored : 78.83 % 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: 1.26 (0.21), residues: 1744 helix: 2.02 (0.22), residues: 568 sheet: 0.59 (0.24), residues: 474 loop : 0.13 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP E 241 HIS 0.002 0.000 HIS A 184 PHE 0.033 0.001 PHE C 417 TYR 0.025 0.001 TYR D 299 ARG 0.005 0.000 ARG N 459 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5585.43 seconds wall clock time: 99 minutes 32.20 seconds (5972.20 seconds total)