Starting phenix.real_space_refine on Wed Mar 4 12:32:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kuy_23041/03_2026/7kuy_23041.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kuy_23041/03_2026/7kuy_23041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kuy_23041/03_2026/7kuy_23041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kuy_23041/03_2026/7kuy_23041.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kuy_23041/03_2026/7kuy_23041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kuy_23041/03_2026/7kuy_23041.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 83 5.16 5 C 8906 2.51 5 N 2177 2.21 5 O 2467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13633 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2698 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2697 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2674 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 4, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2663 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 15, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 5, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "E" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2650 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 3, 'ARG:plan': 3, 'TYR:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2, 'SY9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2, 'SY9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2, 'SY9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'NAG': 2, 'SY9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'SY9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.74, per 1000 atoms: 0.20 Number of scatterers: 13633 At special positions: 0 Unit cell: (91.3, 91.3, 129.48, 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 83 16.00 O 2467 8.00 N 2177 7.00 C 8906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 216 " distance=2.04 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS D 205 " - pdb=" SG CYS D 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 45 " " NAG A 502 " - " ASN A 76 " " NAG B 501 " - " ASN B 45 " " NAG B 502 " - " ASN B 76 " " NAG C 501 " - " ASN C 45 " " NAG C 502 " - " ASN C 76 " " NAG D 501 " - " ASN D 45 " " NAG D 502 " - " ASN D 76 " " NAG E 501 " - " ASN E 220 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 622.9 milliseconds 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3250 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 20 sheets defined 36.1% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 16 through 25 removed outlier: 4.194A pdb=" N ASP A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 81 Processing helix chain 'A' and resid 227 through 235 removed outlier: 3.592A pdb=" N TYR A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 250 removed outlier: 3.843A pdb=" N PHE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 281 removed outlier: 3.961A pdb=" N ARG A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 315 removed outlier: 3.814A pdb=" N TRP A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS A 297 " --> pdb=" O TRP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 416 Proline residue: A 400 - end of helix Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.595A pdb=" N LEU B 97 " --> pdb=" O PRO B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 234 through 249 removed outlier: 3.894A pdb=" N SER B 238 " --> pdb=" O MET B 234 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 277 removed outlier: 4.321A pdb=" N VAL B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 261 " --> pdb=" O PRO B 257 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 288 through 316 removed outlier: 3.517A pdb=" N CYS B 297 " --> pdb=" O TRP B 293 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 298 " --> pdb=" O MET B 294 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 414 removed outlier: 4.170A pdb=" N ALA B 388 " --> pdb=" O PHE B 384 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA B 397 " --> pdb=" O THR B 393 " (cutoff:3.500A) Proline residue: B 400 - end of helix removed outlier: 3.800A pdb=" N PHE B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 26 Processing helix chain 'C' and resid 96 through 100 removed outlier: 3.803A pdb=" N SER C 99 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE C 100 " --> pdb=" O LEU C 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 96 through 100' Processing helix chain 'C' and resid 151 through 154 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 235 through 252 removed outlier: 4.217A pdb=" N PHE C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE C 251 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 276 removed outlier: 3.848A pdb=" N ALA C 261 " --> pdb=" O PRO C 257 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 316 removed outlier: 3.560A pdb=" N ARG C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 416 Proline residue: C 400 - end of helix removed outlier: 3.982A pdb=" N THR C 413 " --> pdb=" O PHE C 409 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 416 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 25 Processing helix chain 'D' and resid 78 through 81 removed outlier: 3.657A pdb=" N ALA D 81 " --> pdb=" O SER D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 78 through 81' Processing helix chain 'D' and resid 151 through 154 removed outlier: 3.775A pdb=" N MET D 154 " --> pdb=" O ASN D 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 151 through 154' Processing helix chain 'D' and resid 228 through 234 Processing helix chain 'D' and resid 234 through 251 removed outlier: 3.802A pdb=" N PHE D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D 251 " --> pdb=" O VAL D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 278 removed outlier: 3.959A pdb=" N ARG D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 314 removed outlier: 3.659A pdb=" N ILE D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU D 298 " --> pdb=" O MET D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 409 removed outlier: 4.276A pdb=" N LYS D 389 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE D 391 " --> pdb=" O ARG D 387 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) Proline residue: D 400 - end of helix Processing helix chain 'E' and resid 32 through 37 Processing helix chain 'E' and resid 92 through 95 removed outlier: 3.610A pdb=" N LYS E 95 " --> pdb=" O PRO E 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 167 through 170 Processing helix chain 'E' and resid 244 through 249 Processing helix chain 'E' and resid 252 through 265 Processing helix chain 'E' and resid 266 through 268 No H-bonds generated for 'chain 'E' and resid 266 through 268' Processing helix chain 'E' and resid 275 through 282 removed outlier: 4.127A pdb=" N LEU E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 298 removed outlier: 4.002A pdb=" N THR E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 329 Processing helix chain 'E' and resid 451 through 474 removed outlier: 3.860A pdb=" N ALA E 457 " --> pdb=" O LEU E 453 " (cutoff:3.500A) Proline residue: E 460 - end of helix removed outlier: 4.347A pdb=" N LEU E 464 " --> pdb=" O PRO E 460 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE E 465 " --> pdb=" O PHE E 461 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE E 466 " --> pdb=" O CYS E 462 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP E 471 " --> pdb=" O ASN E 467 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.475A pdb=" N LEU A 125 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ASP A 64 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N SER A 57 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ARG A 66 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE A 55 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN A 68 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASN A 76 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASN A 45 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL A 44 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLU A 176 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 46 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 114 removed outlier: 4.170A pdb=" N GLY A 112 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ASP A 64 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N SER A 57 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ARG A 66 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE A 55 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN A 68 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASN A 76 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASN A 45 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A 184 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 157 removed outlier: 3.576A pdb=" N GLU A 224 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 160 through 164 removed outlier: 4.070A pdb=" N CYS A 216 " --> pdb=" O CYS A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.620A pdb=" N LEU B 92 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU B 125 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASP B 64 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER B 57 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG B 66 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE B 55 " --> pdb=" O ARG B 66 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN B 68 " --> pdb=" O ASN B 53 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ASN B 76 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN B 45 " --> pdb=" O ASN B 76 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 105 through 107 removed outlier: 5.878A pdb=" N THR B 215 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N GLY B 167 " --> pdb=" O LYS B 213 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N LYS B 213 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 194 through 196 removed outlier: 3.711A pdb=" N GLY B 212 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 90 through 92 removed outlier: 4.414A pdb=" N LEU C 125 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ASP C 64 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER C 57 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG C 66 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE C 55 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN C 68 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASN C 76 " --> pdb=" O ASN C 45 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASN C 45 " --> pdb=" O ASN C 76 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL C 44 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLU C 176 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL C 46 " --> pdb=" O GLU C 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 112 through 114 removed outlier: 3.946A pdb=" N GLY C 112 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ASP C 64 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER C 57 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG C 66 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE C 55 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN C 68 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASN C 76 " --> pdb=" O ASN C 45 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASN C 45 " --> pdb=" O ASN C 76 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N GLN C 184 " --> pdb=" O CYS C 48 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE C 50 " --> pdb=" O GLN C 184 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 105 through 107 removed outlier: 5.813A pdb=" N THR C 215 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N GLY C 167 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N LYS C 213 " --> pdb=" O GLY C 167 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 194 through 196 Processing sheet with id=AB3, first strand: chain 'D' and resid 89 through 92 removed outlier: 4.322A pdb=" N LEU D 125 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LYS D 132 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG D 66 " --> pdb=" O PHE D 55 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE D 55 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN D 68 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN D 76 " --> pdb=" O ASN D 45 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN D 45 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE D 174 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 110 through 114 removed outlier: 3.701A pdb=" N GLY D 112 " --> pdb=" O THR D 142 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG D 66 " --> pdb=" O PHE D 55 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE D 55 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN D 68 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN D 76 " --> pdb=" O ASN D 45 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN D 45 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN D 184 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 105 through 107 Processing sheet with id=AB6, first strand: chain 'D' and resid 105 through 107 Processing sheet with id=AB7, first strand: chain 'D' and resid 207 through 208 Processing sheet with id=AB8, first strand: chain 'E' and resid 68 through 73 removed outlier: 3.639A pdb=" N SER E 68 " --> pdb=" O ASN E 82 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE E 72 " --> pdb=" O ASP E 78 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP E 78 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASP E 148 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU E 141 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL E 108 " --> pdb=" O LEU E 141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 68 through 73 removed outlier: 3.639A pdb=" N SER E 68 " --> pdb=" O ASN E 82 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE E 72 " --> pdb=" O ASP E 78 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP E 78 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG E 86 " --> pdb=" O ASN E 63 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL E 58 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE E 192 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL E 60 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 65 through 66 Processing sheet with id=AC2, first strand: chain 'E' and resid 121 through 123 removed outlier: 5.996A pdb=" N THR E 232 " --> pdb=" O SER E 181 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 2016 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: 2.51 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3300 1.33 - 1.45: 3147 1.45 - 1.58: 7421 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 14003 Sorted by residual: bond pdb=" C1 NAG E 501 " pdb=" O5 NAG E 501 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C ALA D 256 " pdb=" N PRO D 257 " ideal model delta sigma weight residual 1.335 1.378 -0.043 1.36e-02 5.41e+03 9.82e+00 bond pdb=" CAG SY9 D 503 " pdb=" CAV SY9 D 503 " ideal model delta sigma weight residual 1.578 1.522 0.056 2.00e-02 2.50e+03 7.75e+00 bond pdb=" N ILE E 268 " pdb=" CA ILE E 268 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.32e-02 5.74e+03 7.73e+00 bond pdb=" N THR D 265 " pdb=" CA THR D 265 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.77e+00 ... (remaining 13998 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 18466 2.18 - 4.35: 523 4.35 - 6.53: 71 6.53 - 8.70: 34 8.70 - 10.88: 7 Bond angle restraints: 19101 Sorted by residual: angle pdb=" N VAL E 330 " pdb=" CA VAL E 330 " pdb=" C VAL E 330 " ideal model delta sigma weight residual 113.53 108.56 4.97 9.80e-01 1.04e+00 2.58e+01 angle pdb=" C THR B 119 " pdb=" N THR B 120 " pdb=" CA THR B 120 " ideal model delta sigma weight residual 121.54 129.83 -8.29 1.91e+00 2.74e-01 1.88e+01 angle pdb=" C GLN D 193 " pdb=" N PHE D 194 " pdb=" CA PHE D 194 " ideal model delta sigma weight residual 121.54 129.44 -7.90 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C VAL B 118 " pdb=" N THR B 119 " pdb=" CA THR B 119 " ideal model delta sigma weight residual 121.54 129.32 -7.78 1.91e+00 2.74e-01 1.66e+01 angle pdb=" C ASN E 39 " pdb=" N ARG E 40 " pdb=" CA ARG E 40 " ideal model delta sigma weight residual 121.54 129.32 -7.78 1.91e+00 2.74e-01 1.66e+01 ... (remaining 19096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.18: 8051 22.18 - 44.36: 496 44.36 - 66.54: 71 66.54 - 88.72: 14 88.72 - 110.90: 3 Dihedral angle restraints: 8635 sinusoidal: 3626 harmonic: 5009 Sorted by residual: dihedral pdb=" CA LEU E 167 " pdb=" C LEU E 167 " pdb=" N PHE E 168 " pdb=" CA PHE E 168 " ideal model delta harmonic sigma weight residual 180.00 -154.79 -25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ASN B 151 " pdb=" C ASN B 151 " pdb=" N PHE B 152 " pdb=" CA PHE B 152 " ideal model delta harmonic sigma weight residual -180.00 -155.79 -24.21 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA ILE A 69 " pdb=" C ILE A 69 " pdb=" N PHE A 70 " pdb=" CA PHE A 70 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 8632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1982 0.090 - 0.179: 196 0.179 - 0.269: 20 0.269 - 0.358: 11 0.358 - 0.448: 6 Chirality restraints: 2215 Sorted by residual: chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 76 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" NAY SY9 E 502 " pdb=" CAS SY9 E 502 " pdb=" CAV SY9 E 502 " pdb=" CAX SY9 E 502 " both_signs ideal model delta sigma weight residual False -2.12 -2.52 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" NAY SY9 D 503 " pdb=" CAS SY9 D 503 " pdb=" CAV SY9 D 503 " pdb=" CAX SY9 D 503 " both_signs ideal model delta sigma weight residual False -2.12 -2.51 0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 2212 not shown) Planarity restraints: 2361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAA SY9 C 503 " -0.121 2.00e-02 2.50e+03 9.70e-02 1.41e+02 pdb=" CAI SY9 C 503 " 0.037 2.00e-02 2.50e+03 pdb=" CAK SY9 C 503 " -0.016 2.00e-02 2.50e+03 pdb=" CAL SY9 C 503 " -0.082 2.00e-02 2.50e+03 pdb=" NAH SY9 C 503 " 0.183 2.00e-02 2.50e+03 pdb=" OAJ SY9 C 503 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA E 253 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO E 254 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO E 254 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 254 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 118 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C VAL A 118 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL A 118 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 119 " 0.013 2.00e-02 2.50e+03 ... (remaining 2358 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1621 2.75 - 3.28: 12845 3.28 - 3.82: 22025 3.82 - 4.36: 25710 4.36 - 4.90: 45619 Nonbonded interactions: 107820 Sorted by model distance: nonbonded pdb=" OG1 THR B 62 " pdb=" OD2 ASP B 64 " model vdw 2.208 3.040 nonbonded pdb=" OG SER D 285 " pdb=" O GLN E 243 " model vdw 2.218 3.040 nonbonded pdb=" O LEU D 105 " pdb=" OG1 THR E 135 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR E 185 " pdb=" OD1 ASP E 187 " model vdw 2.225 3.040 nonbonded pdb=" OG SER C 285 " pdb=" O GLN D 226 " model vdw 2.235 3.040 ... (remaining 107815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 18 or (resid 19 and (name N or name CA or name \ C or name O or name CB )) or resid 20 through 21 or (resid 22 and (name N or nam \ e CA or name C or name O or name CB )) or resid 23 through 33 or (resid 34 and ( \ name N or name CA or name C or name O or name CB )) or resid 35 through 59 or (r \ esid 60 and (name N or name CA or name C or name O or name CB )) or resid 61 thr \ ough 175 or (resid 176 and (name N or name CA or name C or name O or name CB )) \ or resid 177 through 186 or (resid 187 and (name N or name CA or name C or name \ O or name CB )) or resid 188 through 250 or (resid 251 and (name N or name CA or \ name C or name O or name CB )) or resid 252 through 253 or (resid 254 through 2 \ 56 and (name N or name CA or name C or name O or name CB )) or resid 257 through \ 305 or (resid 306 and (name N or name CA or name C or name O or name CB )) or r \ esid 307 through 315 or (resid 316 through 398 and (name N or name CA or name C \ or name O or name CB )) or resid 399 through 400 or (resid 401 through 402 and ( \ name N or name CA or name C or name O or name CB )) or resid 403 through 408 or \ (resid 409 and (name N or name CA or name C or name O or name CB )) or resid 410 \ through 503)) selection = (chain 'B' and ((resid 15 and (name N or name CA or name C or name O or name CB \ )) or resid 16 through 18 or (resid 19 and (name N or name CA or name C or name \ O or name CB )) or resid 20 through 21 or (resid 22 and (name N or name CA or na \ me C or name O or name CB )) or resid 23 through 33 or (resid 34 and (name N or \ name CA or name C or name O or name CB )) or resid 35 through 175 or (resid 176 \ and (name N or name CA or name C or name O or name CB )) or resid 177 through 18 \ 6 or (resid 187 and (name N or name CA or name C or name O or name CB )) or resi \ d 188 through 250 or (resid 251 and (name N or name CA or name C or name O or na \ me CB )) or resid 252 through 305 or (resid 306 and (name N or name CA or name C \ or name O or name CB )) or resid 307 through 315 or (resid 316 through 398 and \ (name N or name CA or name C or name O or name CB )) or resid 399 through 400 or \ (resid 401 through 402 and (name N or name CA or name C or name O or name CB )) \ or resid 403 through 404 or (resid 405 and (name N or name CA or name C or name \ O or name CB )) or resid 406 through 408 or (resid 409 and (name N or name CA o \ r name C or name O or name CB )) or resid 410 through 503)) selection = (chain 'C' and ((resid 15 and (name N or name CA or name C or name O or name CB \ )) or resid 16 through 21 or (resid 22 and (name N or name CA or name C or name \ O or name CB )) or resid 23 through 59 or (resid 60 and (name N or name CA or na \ me C or name O or name CB )) or resid 61 through 175 or (resid 176 and (name N o \ r name CA or name C or name O or name CB )) or resid 177 through 186 or (resid 1 \ 87 and (name N or name CA or name C or name O or name CB )) or resid 188 through \ 305 or (resid 306 and (name N or name CA or name C or name O or name CB )) or r \ esid 307 through 386 or (resid 387 through 398 and (name N or name CA or name C \ or name O or name CB )) or resid 399 through 404 or (resid 405 and (name N or na \ me CA or name C or name O or name CB )) or resid 406 through 503)) selection = (chain 'D' and ((resid 15 and (name N or name CA or name C or name O or name CB \ )) or resid 16 through 59 or (resid 60 and (name N or name CA or name C or name \ O or name CB )) or resid 61 through 250 or (resid 251 and (name N or name CA or \ name C or name O or name CB )) or resid 252 or (resid 253 through 256 and (name \ N or name CA or name C or name O or name CB )) or resid 257 through 400 or (resi \ d 401 through 402 and (name N or name CA or name C or name O or name CB )) or re \ sid 403 through 404 or (resid 405 and (name N or name CA or name C or name O or \ name CB )) or resid 406 through 408 or (resid 409 and (name N or name CA or name \ C or name O or name CB )) or resid 410 through 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.360 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 : 0.006 0.079 14018 Z= 0.283 Angle : 0.924 10.877 19140 Z= 0.477 Chirality : 0.062 0.448 2215 Planarity : 0.006 0.097 2352 Dihedral : 14.527 110.898 5367 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.14 % Allowed : 11.59 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.24 (0.17), residues: 1674 helix: -1.88 (0.17), residues: 571 sheet: -2.83 (0.23), residues: 390 loop : -3.52 (0.18), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 278 TYR 0.020 0.002 TYR C 135 PHE 0.020 0.002 PHE E 69 TRP 0.023 0.002 TRP A 293 HIS 0.003 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00621 (14003) covalent geometry : angle 0.91400 (19101) SS BOND : bond 0.00493 ( 6) SS BOND : angle 1.81811 ( 12) hydrogen bonds : bond 0.11313 ( 617) hydrogen bonds : angle 6.52882 ( 2016) link_NAG-ASN : bond 0.00567 ( 9) link_NAG-ASN : angle 3.52649 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 262 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.7773 (mtm) cc_final: 0.7079 (mpp) REVERT: B 63 MET cc_start: 0.8910 (mmt) cc_final: 0.8569 (mmt) REVERT: B 172 ASP cc_start: 0.7617 (m-30) cc_final: 0.7307 (m-30) REVERT: B 217 ILE cc_start: 0.9236 (pt) cc_final: 0.8960 (pt) REVERT: C 25 MET cc_start: 0.8487 (ptp) cc_final: 0.8248 (ptp) REVERT: C 82 TYR cc_start: 0.8154 (p90) cc_final: 0.7787 (p90) REVERT: C 197 LYS cc_start: 0.8066 (mmmt) cc_final: 0.7850 (mmtt) REVERT: C 224 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7645 (tm-30) REVERT: C 407 ASN cc_start: 0.8430 (t0) cc_final: 0.8135 (t0) REVERT: E 180 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7638 (mt-10) REVERT: E 223 LYS cc_start: 0.8657 (mmtp) cc_final: 0.8451 (mttm) REVERT: E 235 GLU cc_start: 0.8260 (pt0) cc_final: 0.7872 (pt0) outliers start: 2 outliers final: 1 residues processed: 264 average time/residue: 0.1088 time to fit residues: 42.8810 Evaluate side-chains 196 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0020 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN D 74 GLN E 73 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.100512 restraints weight = 21273.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103940 restraints weight = 10881.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106123 restraints weight = 7166.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.107503 restraints weight = 5508.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.108292 restraints weight = 4660.377| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14018 Z= 0.129 Angle : 0.659 9.830 19140 Z= 0.328 Chirality : 0.045 0.345 2215 Planarity : 0.004 0.057 2352 Dihedral : 8.393 102.778 2336 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.80 % Allowed : 16.52 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.19), residues: 1674 helix: -0.27 (0.21), residues: 559 sheet: -2.26 (0.24), residues: 398 loop : -3.16 (0.20), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 278 TYR 0.016 0.001 TYR E 303 PHE 0.017 0.001 PHE D 249 TRP 0.022 0.001 TRP D 246 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00285 (14003) covalent geometry : angle 0.64904 (19101) SS BOND : bond 0.00363 ( 6) SS BOND : angle 2.40006 ( 12) hydrogen bonds : bond 0.03742 ( 617) hydrogen bonds : angle 5.23828 ( 2016) link_NAG-ASN : bond 0.00251 ( 9) link_NAG-ASN : angle 2.76087 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8183 (t0) cc_final: 0.7913 (t0) REVERT: A 154 MET cc_start: 0.7800 (mtm) cc_final: 0.6985 (mpp) REVERT: B 63 MET cc_start: 0.8973 (mmt) cc_final: 0.8645 (mmt) REVERT: B 172 ASP cc_start: 0.7556 (m-30) cc_final: 0.7248 (m-30) REVERT: C 22 ASP cc_start: 0.8438 (m-30) cc_final: 0.7754 (t0) REVERT: C 82 TYR cc_start: 0.8158 (p90) cc_final: 0.7754 (p90) REVERT: C 224 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7579 (tm-30) REVERT: D 72 ARG cc_start: 0.8121 (tmm-80) cc_final: 0.7901 (ttp80) REVERT: E 116 LEU cc_start: 0.8935 (pp) cc_final: 0.8717 (pp) REVERT: E 180 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7522 (mt-10) REVERT: E 197 ASP cc_start: 0.6304 (p0) cc_final: 0.6012 (p0) REVERT: E 235 GLU cc_start: 0.8261 (pt0) cc_final: 0.7740 (pt0) outliers start: 26 outliers final: 13 residues processed: 238 average time/residue: 0.0996 time to fit residues: 35.8147 Evaluate side-chains 208 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 250 TRP Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 260 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 158 optimal weight: 0.6980 chunk 75 optimal weight: 0.2980 chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN C 68 ASN ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 222 HIS E 73 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.125556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.103127 restraints weight = 21397.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.106699 restraints weight = 10808.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.108921 restraints weight = 7011.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.110281 restraints weight = 5364.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.111031 restraints weight = 4535.454| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14018 Z= 0.110 Angle : 0.609 9.756 19140 Z= 0.303 Chirality : 0.044 0.340 2215 Planarity : 0.003 0.050 2352 Dihedral : 7.575 103.222 2336 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.71 % Allowed : 18.32 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.20), residues: 1674 helix: 0.50 (0.22), residues: 560 sheet: -1.74 (0.26), residues: 386 loop : -2.81 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 278 TYR 0.016 0.001 TYR B 308 PHE 0.014 0.001 PHE D 249 TRP 0.030 0.001 TRP D 246 HIS 0.002 0.000 HIS D 116 Details of bonding type rmsd covalent geometry : bond 0.00238 (14003) covalent geometry : angle 0.59925 (19101) SS BOND : bond 0.00246 ( 6) SS BOND : angle 2.05314 ( 12) hydrogen bonds : bond 0.03405 ( 617) hydrogen bonds : angle 4.89568 ( 2016) link_NAG-ASN : bond 0.00357 ( 9) link_NAG-ASN : angle 2.60483 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8197 (t0) cc_final: 0.7883 (t0) REVERT: A 154 MET cc_start: 0.7675 (mtm) cc_final: 0.6851 (mpp) REVERT: B 63 MET cc_start: 0.8951 (mmt) cc_final: 0.8643 (mmt) REVERT: C 22 ASP cc_start: 0.8337 (m-30) cc_final: 0.7754 (t0) REVERT: C 82 TYR cc_start: 0.8150 (p90) cc_final: 0.7745 (p90) REVERT: D 72 ARG cc_start: 0.8108 (tmm-80) cc_final: 0.7816 (ttp80) REVERT: E 113 TYR cc_start: 0.8464 (t80) cc_final: 0.8024 (t80) REVERT: E 116 LEU cc_start: 0.8883 (pp) cc_final: 0.8661 (pp) REVERT: E 197 ASP cc_start: 0.6287 (p0) cc_final: 0.6044 (p0) REVERT: E 235 GLU cc_start: 0.8240 (pt0) cc_final: 0.7754 (pt0) outliers start: 39 outliers final: 20 residues processed: 252 average time/residue: 0.1010 time to fit residues: 38.9942 Evaluate side-chains 221 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 214 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 107 optimal weight: 0.2980 chunk 117 optimal weight: 7.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN E 73 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.123619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.101142 restraints weight = 21449.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.104661 restraints weight = 10892.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.106854 restraints weight = 7108.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.108088 restraints weight = 5453.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.109004 restraints weight = 4671.922| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14018 Z= 0.154 Angle : 0.624 9.790 19140 Z= 0.310 Chirality : 0.045 0.338 2215 Planarity : 0.004 0.054 2352 Dihedral : 7.225 100.828 2332 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.54 % Allowed : 19.85 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.20), residues: 1674 helix: 0.78 (0.22), residues: 559 sheet: -1.57 (0.26), residues: 387 loop : -2.69 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 48 TYR 0.015 0.001 TYR E 303 PHE 0.012 0.001 PHE E 69 TRP 0.046 0.001 TRP D 246 HIS 0.002 0.000 HIS D 116 Details of bonding type rmsd covalent geometry : bond 0.00359 (14003) covalent geometry : angle 0.61462 (19101) SS BOND : bond 0.00240 ( 6) SS BOND : angle 2.11126 ( 12) hydrogen bonds : bond 0.03476 ( 617) hydrogen bonds : angle 4.81373 ( 2016) link_NAG-ASN : bond 0.00227 ( 9) link_NAG-ASN : angle 2.56718 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 200 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8187 (t0) cc_final: 0.7868 (t0) REVERT: A 154 MET cc_start: 0.7754 (mtm) cc_final: 0.6967 (mpp) REVERT: A 176 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7265 (mm-30) REVERT: B 63 MET cc_start: 0.8937 (mmt) cc_final: 0.8630 (mmt) REVERT: B 172 ASP cc_start: 0.7546 (m-30) cc_final: 0.7164 (m-30) REVERT: C 22 ASP cc_start: 0.8337 (m-30) cc_final: 0.7813 (t0) REVERT: C 82 TYR cc_start: 0.8182 (p90) cc_final: 0.7737 (p90) REVERT: C 224 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7430 (tm-30) REVERT: C 285 SER cc_start: 0.8993 (OUTLIER) cc_final: 0.8398 (t) REVERT: E 113 TYR cc_start: 0.8481 (t80) cc_final: 0.8068 (t80) REVERT: E 116 LEU cc_start: 0.8899 (pp) cc_final: 0.8680 (pp) REVERT: E 197 ASP cc_start: 0.6343 (p0) cc_final: 0.6072 (p0) REVERT: E 235 GLU cc_start: 0.8287 (pt0) cc_final: 0.7732 (pt0) outliers start: 51 outliers final: 31 residues processed: 240 average time/residue: 0.0973 time to fit residues: 35.7456 Evaluate side-chains 216 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 329 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 40.0000 chunk 84 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 96 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN E 73 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.102022 restraints weight = 21489.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.105557 restraints weight = 10956.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.107777 restraints weight = 7129.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.108994 restraints weight = 5468.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109906 restraints weight = 4696.701| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14018 Z= 0.130 Angle : 0.615 9.768 19140 Z= 0.303 Chirality : 0.045 0.339 2215 Planarity : 0.003 0.052 2352 Dihedral : 7.026 99.732 2332 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.40 % Allowed : 21.10 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.21), residues: 1674 helix: 0.98 (0.23), residues: 558 sheet: -1.42 (0.26), residues: 383 loop : -2.58 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 48 TYR 0.015 0.001 TYR E 303 PHE 0.011 0.001 PHE D 302 TRP 0.058 0.001 TRP D 246 HIS 0.002 0.000 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00299 (14003) covalent geometry : angle 0.60672 (19101) SS BOND : bond 0.00413 ( 6) SS BOND : angle 1.87967 ( 12) hydrogen bonds : bond 0.03348 ( 617) hydrogen bonds : angle 4.64988 ( 2016) link_NAG-ASN : bond 0.00279 ( 9) link_NAG-ASN : angle 2.46488 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8254 (t0) cc_final: 0.7872 (t0) REVERT: A 154 MET cc_start: 0.7734 (mtm) cc_final: 0.6882 (mpp) REVERT: B 63 MET cc_start: 0.8909 (mmt) cc_final: 0.8634 (mmt) REVERT: B 172 ASP cc_start: 0.7549 (m-30) cc_final: 0.7181 (m-30) REVERT: C 22 ASP cc_start: 0.8319 (m-30) cc_final: 0.7853 (t0) REVERT: C 82 TYR cc_start: 0.8181 (p90) cc_final: 0.7737 (p90) REVERT: C 224 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7226 (tm-30) REVERT: C 285 SER cc_start: 0.8973 (OUTLIER) cc_final: 0.8442 (t) REVERT: D 72 ARG cc_start: 0.7754 (ttp80) cc_final: 0.7104 (ttp80) REVERT: D 138 ARG cc_start: 0.9075 (ttt-90) cc_final: 0.8693 (ttt-90) REVERT: E 113 TYR cc_start: 0.8454 (t80) cc_final: 0.8052 (t80) REVERT: E 116 LEU cc_start: 0.8899 (pp) cc_final: 0.8689 (pp) REVERT: E 197 ASP cc_start: 0.6374 (p0) cc_final: 0.6103 (p0) REVERT: E 235 GLU cc_start: 0.8288 (pt0) cc_final: 0.7750 (pt0) outliers start: 49 outliers final: 32 residues processed: 240 average time/residue: 0.1002 time to fit residues: 36.9073 Evaluate side-chains 226 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 329 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 11 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 163 optimal weight: 20.0000 chunk 139 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN E 73 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.100293 restraints weight = 21474.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103720 restraints weight = 11024.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.105903 restraints weight = 7278.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.107209 restraints weight = 5613.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.108081 restraints weight = 4794.082| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14018 Z= 0.171 Angle : 0.631 9.787 19140 Z= 0.312 Chirality : 0.045 0.338 2215 Planarity : 0.003 0.055 2352 Dihedral : 7.003 97.293 2332 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.02 % Allowed : 21.72 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.21), residues: 1674 helix: 0.93 (0.23), residues: 563 sheet: -1.39 (0.26), residues: 387 loop : -2.51 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 259 TYR 0.014 0.001 TYR E 303 PHE 0.012 0.001 PHE E 69 TRP 0.058 0.001 TRP D 246 HIS 0.002 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00399 (14003) covalent geometry : angle 0.62247 (19101) SS BOND : bond 0.00444 ( 6) SS BOND : angle 2.04780 ( 12) hydrogen bonds : bond 0.03451 ( 617) hydrogen bonds : angle 4.64888 ( 2016) link_NAG-ASN : bond 0.00257 ( 9) link_NAG-ASN : angle 2.50532 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 203 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8419 (mttt) cc_final: 0.7997 (ptmm) REVERT: A 117 ASP cc_start: 0.8316 (t0) cc_final: 0.7914 (t0) REVERT: A 154 MET cc_start: 0.7839 (mtm) cc_final: 0.7122 (mpp) REVERT: B 63 MET cc_start: 0.8911 (mmt) cc_final: 0.8631 (mmt) REVERT: B 172 ASP cc_start: 0.7584 (m-30) cc_final: 0.7215 (m-30) REVERT: C 22 ASP cc_start: 0.8323 (m-30) cc_final: 0.7850 (t0) REVERT: C 224 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7292 (tm-30) REVERT: C 285 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8635 (t) REVERT: C 286 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.8614 (p90) REVERT: D 138 ARG cc_start: 0.9100 (ttt-90) cc_final: 0.8705 (ttt-90) REVERT: D 180 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8130 (t0) REVERT: D 241 ILE cc_start: 0.8305 (mm) cc_final: 0.8093 (mm) REVERT: E 113 TYR cc_start: 0.8484 (t80) cc_final: 0.8076 (t80) REVERT: E 116 LEU cc_start: 0.8922 (pp) cc_final: 0.8714 (pp) REVERT: E 235 GLU cc_start: 0.8305 (pt0) cc_final: 0.7748 (pt0) outliers start: 58 outliers final: 37 residues processed: 245 average time/residue: 0.0963 time to fit residues: 36.6856 Evaluate side-chains 220 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 329 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 37 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 152 optimal weight: 0.0970 chunk 141 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN E 73 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.101594 restraints weight = 21256.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.105073 restraints weight = 10931.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.107251 restraints weight = 7208.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.108630 restraints weight = 5547.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.109263 restraints weight = 4706.388| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14018 Z= 0.135 Angle : 0.615 9.771 19140 Z= 0.305 Chirality : 0.045 0.338 2215 Planarity : 0.003 0.052 2352 Dihedral : 6.877 95.939 2332 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.61 % Allowed : 22.69 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.21), residues: 1674 helix: 1.04 (0.23), residues: 563 sheet: -1.25 (0.27), residues: 383 loop : -2.39 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 126 TYR 0.033 0.001 TYR B 229 PHE 0.030 0.001 PHE C 249 TRP 0.057 0.001 TRP D 246 HIS 0.002 0.000 HIS D 116 Details of bonding type rmsd covalent geometry : bond 0.00311 (14003) covalent geometry : angle 0.60688 (19101) SS BOND : bond 0.00243 ( 6) SS BOND : angle 1.93244 ( 12) hydrogen bonds : bond 0.03311 ( 617) hydrogen bonds : angle 4.56805 ( 2016) link_NAG-ASN : bond 0.00284 ( 9) link_NAG-ASN : angle 2.42848 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 200 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8403 (mttt) cc_final: 0.7996 (ptmm) REVERT: A 117 ASP cc_start: 0.8239 (t0) cc_final: 0.7826 (t0) REVERT: A 154 MET cc_start: 0.7851 (mtm) cc_final: 0.7194 (mpp) REVERT: B 63 MET cc_start: 0.8869 (mmt) cc_final: 0.8604 (mmt) REVERT: C 22 ASP cc_start: 0.8295 (m-30) cc_final: 0.7832 (t0) REVERT: C 170 MET cc_start: 0.8403 (tpp) cc_final: 0.7868 (mmt) REVERT: C 224 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7251 (tm-30) REVERT: C 285 SER cc_start: 0.8990 (OUTLIER) cc_final: 0.8592 (t) REVERT: C 286 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.8681 (p90) REVERT: E 113 TYR cc_start: 0.8447 (t80) cc_final: 0.7988 (t80) REVERT: E 116 LEU cc_start: 0.8901 (pp) cc_final: 0.8693 (pp) REVERT: E 235 GLU cc_start: 0.8304 (pt0) cc_final: 0.7758 (pt0) outliers start: 52 outliers final: 37 residues processed: 238 average time/residue: 0.0883 time to fit residues: 33.3858 Evaluate side-chains 224 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 109 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN E 73 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099869 restraints weight = 21347.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.103270 restraints weight = 10964.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.105415 restraints weight = 7230.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.106655 restraints weight = 5598.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.107577 restraints weight = 4814.955| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14018 Z= 0.179 Angle : 0.646 9.800 19140 Z= 0.321 Chirality : 0.045 0.337 2215 Planarity : 0.004 0.054 2352 Dihedral : 6.901 92.771 2332 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.54 % Allowed : 22.97 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.21), residues: 1674 helix: 0.96 (0.23), residues: 567 sheet: -1.40 (0.26), residues: 396 loop : -2.35 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 259 TYR 0.025 0.001 TYR B 229 PHE 0.029 0.002 PHE A 249 TRP 0.042 0.001 TRP D 246 HIS 0.002 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00421 (14003) covalent geometry : angle 0.63746 (19101) SS BOND : bond 0.00313 ( 6) SS BOND : angle 1.91751 ( 12) hydrogen bonds : bond 0.03527 ( 617) hydrogen bonds : angle 4.62382 ( 2016) link_NAG-ASN : bond 0.00256 ( 9) link_NAG-ASN : angle 2.50919 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8402 (mttt) cc_final: 0.8002 (ptmm) REVERT: A 117 ASP cc_start: 0.8294 (t0) cc_final: 0.7879 (t0) REVERT: A 154 MET cc_start: 0.7921 (mtm) cc_final: 0.7321 (mpp) REVERT: B 63 MET cc_start: 0.8885 (mmt) cc_final: 0.8618 (mmt) REVERT: C 22 ASP cc_start: 0.8344 (m-30) cc_final: 0.7853 (t0) REVERT: C 224 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7550 (tm-30) REVERT: C 285 SER cc_start: 0.9013 (OUTLIER) cc_final: 0.8632 (t) REVERT: C 286 TYR cc_start: 0.9136 (OUTLIER) cc_final: 0.8804 (p90) REVERT: D 193 GLN cc_start: 0.8185 (tt0) cc_final: 0.7754 (pm20) REVERT: D 285 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8420 (t) REVERT: E 113 TYR cc_start: 0.8460 (t80) cc_final: 0.8036 (t80) REVERT: E 116 LEU cc_start: 0.8943 (pp) cc_final: 0.8732 (pp) REVERT: E 235 GLU cc_start: 0.8306 (pt0) cc_final: 0.7738 (pt0) REVERT: E 291 CYS cc_start: 0.7980 (m) cc_final: 0.7612 (m) outliers start: 51 outliers final: 41 residues processed: 226 average time/residue: 0.0933 time to fit residues: 33.4492 Evaluate side-chains 226 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 92 optimal weight: 0.0370 chunk 34 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.101727 restraints weight = 21305.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105222 restraints weight = 10902.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.107405 restraints weight = 7145.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.108763 restraints weight = 5500.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.109482 restraints weight = 4681.497| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14018 Z= 0.132 Angle : 0.626 9.798 19140 Z= 0.310 Chirality : 0.045 0.338 2215 Planarity : 0.003 0.052 2352 Dihedral : 6.772 92.270 2332 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.33 % Allowed : 23.46 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.21), residues: 1674 helix: 1.04 (0.23), residues: 572 sheet: -1.28 (0.26), residues: 396 loop : -2.29 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 259 TYR 0.025 0.001 TYR B 229 PHE 0.037 0.001 PHE B 249 TRP 0.047 0.001 TRP D 246 HIS 0.002 0.000 HIS D 116 Details of bonding type rmsd covalent geometry : bond 0.00305 (14003) covalent geometry : angle 0.61871 (19101) SS BOND : bond 0.00191 ( 6) SS BOND : angle 1.81028 ( 12) hydrogen bonds : bond 0.03342 ( 617) hydrogen bonds : angle 4.52843 ( 2016) link_NAG-ASN : bond 0.00289 ( 9) link_NAG-ASN : angle 2.41481 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8394 (mttt) cc_final: 0.7998 (ptmm) REVERT: A 117 ASP cc_start: 0.8179 (t0) cc_final: 0.7805 (t0) REVERT: A 154 MET cc_start: 0.7812 (mtm) cc_final: 0.7111 (mpp) REVERT: B 63 MET cc_start: 0.8860 (mmt) cc_final: 0.8619 (mmt) REVERT: B 233 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7771 (tm-30) REVERT: C 22 ASP cc_start: 0.8321 (m-30) cc_final: 0.7842 (t0) REVERT: C 224 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7280 (tm-30) REVERT: C 285 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8399 (t) REVERT: C 286 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8827 (p90) REVERT: D 285 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8380 (t) REVERT: E 113 TYR cc_start: 0.8421 (t80) cc_final: 0.7998 (t80) REVERT: E 116 LEU cc_start: 0.8902 (pp) cc_final: 0.8687 (pp) REVERT: E 235 GLU cc_start: 0.8287 (pt0) cc_final: 0.7726 (pt0) REVERT: E 291 CYS cc_start: 0.7971 (m) cc_final: 0.7609 (m) outliers start: 48 outliers final: 39 residues processed: 230 average time/residue: 0.0940 time to fit residues: 34.0081 Evaluate side-chains 225 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 154 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 136 optimal weight: 0.0970 chunk 135 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 119 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN E 73 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103267 restraints weight = 21233.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.106682 restraints weight = 10866.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.108877 restraints weight = 7176.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.110108 restraints weight = 5516.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111035 restraints weight = 4742.712| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14018 Z= 0.116 Angle : 0.634 10.638 19140 Z= 0.313 Chirality : 0.045 0.336 2215 Planarity : 0.003 0.051 2352 Dihedral : 6.642 91.122 2332 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.78 % Allowed : 24.36 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.21), residues: 1674 helix: 1.10 (0.22), residues: 572 sheet: -1.01 (0.27), residues: 395 loop : -2.22 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 259 TYR 0.020 0.001 TYR B 229 PHE 0.037 0.001 PHE B 249 TRP 0.046 0.001 TRP D 246 HIS 0.003 0.000 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00262 (14003) covalent geometry : angle 0.62489 (19101) SS BOND : bond 0.00652 ( 6) SS BOND : angle 2.85821 ( 12) hydrogen bonds : bond 0.03238 ( 617) hydrogen bonds : angle 4.51000 ( 2016) link_NAG-ASN : bond 0.00317 ( 9) link_NAG-ASN : angle 2.30079 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8350 (mttt) cc_final: 0.7911 (ptmm) REVERT: A 117 ASP cc_start: 0.8113 (t0) cc_final: 0.7740 (t0) REVERT: A 154 MET cc_start: 0.7750 (mtm) cc_final: 0.7031 (mpp) REVERT: B 63 MET cc_start: 0.8819 (mmt) cc_final: 0.8546 (mmm) REVERT: B 308 TYR cc_start: 0.8029 (t80) cc_final: 0.7741 (t80) REVERT: C 22 ASP cc_start: 0.8249 (m-30) cc_final: 0.7838 (t0) REVERT: C 224 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7205 (tm-30) REVERT: C 285 SER cc_start: 0.8973 (OUTLIER) cc_final: 0.8351 (t) REVERT: D 117 ASP cc_start: 0.7854 (p0) cc_final: 0.7351 (p0) REVERT: D 193 GLN cc_start: 0.8162 (tt0) cc_final: 0.7605 (pm20) REVERT: D 249 PHE cc_start: 0.8163 (p90) cc_final: 0.7954 (p90) REVERT: D 285 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8270 (t) REVERT: E 113 TYR cc_start: 0.8386 (t80) cc_final: 0.7985 (t80) REVERT: E 116 LEU cc_start: 0.8862 (pp) cc_final: 0.8649 (pp) REVERT: E 235 GLU cc_start: 0.8254 (pt0) cc_final: 0.7733 (pt0) REVERT: E 291 CYS cc_start: 0.7909 (m) cc_final: 0.7577 (m) outliers start: 40 outliers final: 33 residues processed: 238 average time/residue: 0.0908 time to fit residues: 33.8268 Evaluate side-chains 228 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 163 optimal weight: 30.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.123805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.101284 restraints weight = 21467.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104754 restraints weight = 10981.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106968 restraints weight = 7217.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.108365 restraints weight = 5528.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.109134 restraints weight = 4679.218| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14018 Z= 0.168 Angle : 0.659 10.564 19140 Z= 0.326 Chirality : 0.046 0.336 2215 Planarity : 0.004 0.098 2352 Dihedral : 6.691 88.055 2332 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.78 % Allowed : 24.91 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.21), residues: 1674 helix: 1.10 (0.22), residues: 568 sheet: -1.09 (0.27), residues: 396 loop : -2.23 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 259 TYR 0.016 0.001 TYR B 230 PHE 0.037 0.002 PHE B 249 TRP 0.051 0.002 TRP D 246 HIS 0.002 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00396 (14003) covalent geometry : angle 0.64968 (19101) SS BOND : bond 0.00262 ( 6) SS BOND : angle 2.93417 ( 12) hydrogen bonds : bond 0.03426 ( 617) hydrogen bonds : angle 4.59184 ( 2016) link_NAG-ASN : bond 0.00253 ( 9) link_NAG-ASN : angle 2.40588 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1909.82 seconds wall clock time: 33 minutes 53.92 seconds (2033.92 seconds total)