Starting phenix.real_space_refine on Thu Jul 31 16:44:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kuy_23041/07_2025/7kuy_23041.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kuy_23041/07_2025/7kuy_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7kuy_23041/07_2025/7kuy_23041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kuy_23041/07_2025/7kuy_23041.map" model { file = "/net/cci-nas-00/data/ceres_data/7kuy_23041/07_2025/7kuy_23041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kuy_23041/07_2025/7kuy_23041.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'ARG:plan': 2, 'ASP:plan': 1} 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, 'ARG:plan': 3, 'ASP: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: {'PHE:plan': 2, 'ARG:plan': 4, 'ASP:plan': 4} 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: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 4} 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, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} 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: 8.56, per 1000 atoms: 0.63 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: 3.28 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.66 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: 4.42 Time building geometry restraints manager: 3.79 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 419 or resid 501 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 419 or resid 501 through 5 \ 03)) 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 419 or resid 501 th \ rough 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 419 or resid 501 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: 1.260 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: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.230 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.880 ------------------------------------------------------------------------------- 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 : 7.93 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (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 TRP 0.023 0.002 TRP A 293 HIS 0.003 0.001 HIS E 132 PHE 0.020 0.002 PHE E 69 TYR 0.020 0.002 TYR C 135 ARG 0.005 0.000 ARG D 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 9) link_NAG-ASN : angle 3.52649 ( 27) hydrogen bonds : bond 0.11313 ( 617) hydrogen bonds : angle 6.52882 ( 2016) SS BOND : bond 0.00493 ( 6) SS BOND : angle 1.81811 ( 12) covalent geometry : bond 0.00621 (14003) covalent geometry : angle 0.91400 (19101) *********************** 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 : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.7773 (mtm) cc_final: 0.7078 (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: 0.7851 (mmtt) REVERT: C 224 GLU cc_start: 0.7947 (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: 0.8259 (pt0) cc_final: 0.7872 (pt0) outliers start: 2 outliers final: 1 residues processed: 264 average time/residue: 0.2511 time to fit residues: 98.4093 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 : 1.409 ------------------------------------------------------------------------------- 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 139 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 129 optimal weight: 30.0000 chunk 50 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 D 222 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.100502 restraints weight = 21293.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103941 restraints weight = 10902.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.106127 restraints weight = 7183.150| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14018 Z= 0.134 Angle : 0.660 9.759 19140 Z= 0.328 Chirality : 0.045 0.345 2215 Planarity : 0.004 0.058 2352 Dihedral : 8.269 102.567 2336 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.80 % Allowed : 16.66 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.19), residues: 1674 helix: -0.25 (0.21), residues: 559 sheet: -2.26 (0.24), residues: 398 loop : -3.15 (0.20), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 246 HIS 0.003 0.001 HIS B 116 PHE 0.017 0.001 PHE D 249 TYR 0.016 0.001 TYR E 303 ARG 0.007 0.000 ARG B 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 9) link_NAG-ASN : angle 2.74973 ( 27) hydrogen bonds : bond 0.03754 ( 617) hydrogen bonds : angle 5.20253 ( 2016) SS BOND : bond 0.00294 ( 6) SS BOND : angle 2.29764 ( 12) covalent geometry : bond 0.00298 (14003) covalent geometry : angle 0.65028 (19101) *********************** 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 245 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8200 (t0) cc_final: 0.7934 (t0) REVERT: A 154 MET cc_start: 0.7788 (mtm) cc_final: 0.6971 (mpp) REVERT: B 63 MET cc_start: 0.8974 (mmt) cc_final: 0.8645 (mmt) REVERT: B 172 ASP cc_start: 0.7578 (m-30) cc_final: 0.7270 (m-30) REVERT: C 22 ASP cc_start: 0.8465 (m-30) cc_final: 0.7763 (t0) REVERT: C 82 TYR cc_start: 0.8203 (p90) cc_final: 0.7788 (p90) REVERT: C 224 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7605 (tm-30) REVERT: D 72 ARG cc_start: 0.8122 (tmm-80) cc_final: 0.7915 (ttp80) REVERT: E 116 LEU cc_start: 0.8940 (pp) cc_final: 0.8721 (pp) REVERT: E 180 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7529 (mt-10) REVERT: E 197 ASP cc_start: 0.6352 (p0) cc_final: 0.6061 (p0) REVERT: E 235 GLU cc_start: 0.8243 (pt0) cc_final: 0.7726 (pt0) outliers start: 26 outliers final: 14 residues processed: 239 average time/residue: 0.2397 time to fit residues: 85.9252 Evaluate side-chains 212 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 1.442 ------------------------------------------------------------------------------- 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 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 183 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 214 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 101 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 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 = 0.3454 r_free = 0.3454 target = 0.119958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.097434 restraints weight = 21528.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.100795 restraints weight = 11008.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.102948 restraints weight = 7288.804| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14018 Z= 0.207 Angle : 0.659 9.836 19140 Z= 0.330 Chirality : 0.046 0.340 2215 Planarity : 0.004 0.058 2352 Dihedral : 7.843 101.305 2336 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.85 % Allowed : 19.01 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.20), residues: 1674 helix: 0.30 (0.22), residues: 563 sheet: -2.10 (0.24), residues: 403 loop : -2.97 (0.20), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 246 HIS 0.003 0.001 HIS B 116 PHE 0.014 0.002 PHE E 69 TYR 0.016 0.001 TYR B 229 ARG 0.007 0.000 ARG E 48 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 9) link_NAG-ASN : angle 2.83531 ( 27) hydrogen bonds : bond 0.03857 ( 617) hydrogen bonds : angle 5.07202 ( 2016) SS BOND : bond 0.00419 ( 6) SS BOND : angle 2.13250 ( 12) covalent geometry : bond 0.00488 (14003) covalent geometry : angle 0.64883 (19101) *********************** 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 248 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8210 (t0) cc_final: 0.7968 (t0) REVERT: A 154 MET cc_start: 0.7879 (mtm) cc_final: 0.7074 (mpp) REVERT: B 63 MET cc_start: 0.8987 (mmt) cc_final: 0.8681 (mmt) REVERT: B 82 TYR cc_start: 0.7724 (p90) cc_final: 0.7488 (p90) REVERT: C 22 ASP cc_start: 0.8458 (m-30) cc_final: 0.7773 (t0) REVERT: C 224 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7686 (tm-30) REVERT: D 72 ARG cc_start: 0.8205 (tmm-80) cc_final: 0.7840 (ttp-170) REVERT: E 113 TYR cc_start: 0.8530 (t80) cc_final: 0.8043 (t80) REVERT: E 197 ASP cc_start: 0.6377 (p0) cc_final: 0.6116 (p0) REVERT: E 235 GLU cc_start: 0.8279 (pt0) cc_final: 0.7770 (pt0) outliers start: 41 outliers final: 29 residues processed: 237 average time/residue: 0.2313 time to fit residues: 82.7225 Evaluate side-chains 220 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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 418 ARG 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 250 TRP 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 197 LYS 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 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 164 GLU 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 128 SER Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 228 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 92 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.123338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.100718 restraints weight = 21275.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.104215 restraints weight = 10895.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.106412 restraints weight = 7153.596| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1605 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= 0.131 Angle : 0.626 9.767 19140 Z= 0.311 Chirality : 0.044 0.335 2215 Planarity : 0.004 0.054 2352 Dihedral : 7.527 101.292 2336 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.54 % Allowed : 20.12 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.20), residues: 1674 helix: 0.67 (0.22), residues: 563 sheet: -1.76 (0.25), residues: 395 loop : -2.74 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP D 246 HIS 0.002 0.000 HIS B 116 PHE 0.012 0.001 PHE D 249 TYR 0.015 0.001 TYR E 303 ARG 0.008 0.000 ARG E 48 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 9) link_NAG-ASN : angle 2.65188 ( 27) hydrogen bonds : bond 0.03555 ( 617) hydrogen bonds : angle 4.86952 ( 2016) SS BOND : bond 0.00284 ( 6) SS BOND : angle 2.01631 ( 12) covalent geometry : bond 0.00296 (14003) covalent geometry : angle 0.61609 (19101) *********************** 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 250 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 199 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8188 (t0) cc_final: 0.7885 (t0) REVERT: A 154 MET cc_start: 0.7785 (mtm) cc_final: 0.6969 (mpp) REVERT: B 63 MET cc_start: 0.8961 (mmt) cc_final: 0.8678 (mmt) REVERT: C 22 ASP cc_start: 0.8398 (m-30) cc_final: 0.7779 (t0) REVERT: C 285 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8388 (t) REVERT: D 72 ARG cc_start: 0.8182 (tmm-80) cc_final: 0.7861 (ttp80) REVERT: E 113 TYR cc_start: 0.8484 (t80) cc_final: 0.8074 (t80) REVERT: E 116 LEU cc_start: 0.8959 (pp) cc_final: 0.8726 (pp) REVERT: E 197 ASP cc_start: 0.6402 (p0) cc_final: 0.6115 (p0) REVERT: E 235 GLU cc_start: 0.8278 (pt0) cc_final: 0.7752 (pt0) REVERT: E 268 ILE cc_start: 0.8322 (mm) cc_final: 0.8114 (mt) outliers start: 51 outliers final: 31 residues processed: 241 average time/residue: 0.2456 time to fit residues: 88.2922 Evaluate side-chains 222 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 215 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 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 197 LYS 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 76 THR 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 223 LYS Chi-restraints excluded: chain E residue 323 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.123054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.100349 restraints weight = 21368.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103837 restraints weight = 10994.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.106029 restraints weight = 7217.162| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14018 Z= 0.147 Angle : 0.627 9.796 19140 Z= 0.311 Chirality : 0.045 0.339 2215 Planarity : 0.004 0.053 2352 Dihedral : 7.150 99.420 2332 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.02 % Allowed : 21.37 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.21), residues: 1674 helix: 0.87 (0.23), residues: 558 sheet: -1.56 (0.26), residues: 387 loop : -2.61 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP D 246 HIS 0.002 0.000 HIS B 116 PHE 0.012 0.001 PHE E 69 TYR 0.016 0.001 TYR B 229 ARG 0.009 0.000 ARG E 48 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 9) link_NAG-ASN : angle 2.57926 ( 27) hydrogen bonds : bond 0.03510 ( 617) hydrogen bonds : angle 4.73623 ( 2016) SS BOND : bond 0.00200 ( 6) SS BOND : angle 1.81319 ( 12) covalent geometry : bond 0.00340 (14003) covalent geometry : angle 0.61829 (19101) *********************** 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 258 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 200 time to evaluate : 1.627 Fit side-chains revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8306 (t0) cc_final: 0.7949 (t0) REVERT: A 154 MET cc_start: 0.7817 (mtm) cc_final: 0.6967 (mpp) REVERT: B 63 MET cc_start: 0.8918 (mmt) cc_final: 0.8666 (mmt) REVERT: B 82 TYR cc_start: 0.7745 (p90) cc_final: 0.7527 (p90) REVERT: C 22 ASP cc_start: 0.8373 (m-30) cc_final: 0.7821 (t0) REVERT: C 224 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7466 (tm-30) REVERT: C 285 SER cc_start: 0.8990 (OUTLIER) cc_final: 0.8447 (t) REVERT: C 286 TYR cc_start: 0.9114 (OUTLIER) cc_final: 0.8818 (p90) REVERT: D 72 ARG cc_start: 0.8170 (tmm-80) cc_final: 0.7759 (ttp-110) REVERT: D 84 GLU cc_start: 0.7264 (pm20) cc_final: 0.6908 (pt0) REVERT: E 113 TYR cc_start: 0.8491 (t80) cc_final: 0.8076 (t80) REVERT: E 197 ASP cc_start: 0.6448 (p0) cc_final: 0.6161 (p0) REVERT: E 235 GLU cc_start: 0.8290 (pt0) cc_final: 0.7736 (pt0) REVERT: E 244 VAL cc_start: 0.8464 (m) cc_final: 0.8216 (t) outliers start: 58 outliers final: 40 residues processed: 246 average time/residue: 0.2399 time to fit residues: 90.1562 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 : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 GLN 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 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 265 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 68 ASN 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 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 81 VAL Chi-restraints excluded: chain E residue 108 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 65 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.124273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.101602 restraints weight = 21495.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.105109 restraints weight = 10936.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.107344 restraints weight = 7147.907| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14018 Z= 0.125 Angle : 0.619 9.789 19140 Z= 0.306 Chirality : 0.045 0.337 2215 Planarity : 0.004 0.052 2352 Dihedral : 7.012 98.667 2332 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.89 % Allowed : 22.14 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.21), residues: 1674 helix: 0.95 (0.23), residues: 558 sheet: -1.37 (0.27), residues: 383 loop : -2.52 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP D 246 HIS 0.002 0.000 HIS B 116 PHE 0.029 0.001 PHE C 249 TYR 0.015 0.001 TYR E 303 ARG 0.009 0.000 ARG D 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 9) link_NAG-ASN : angle 2.48189 ( 27) hydrogen bonds : bond 0.03401 ( 617) hydrogen bonds : angle 4.62264 ( 2016) SS BOND : bond 0.00266 ( 6) SS BOND : angle 1.96481 ( 12) covalent geometry : bond 0.00285 (14003) covalent geometry : angle 0.61029 (19101) *********************** 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 251 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 195 time to evaluate : 1.555 Fit side-chains revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8283 (t0) cc_final: 0.7881 (t0) REVERT: A 154 MET cc_start: 0.7803 (mtm) cc_final: 0.7069 (mpp) REVERT: B 63 MET cc_start: 0.8898 (mmt) cc_final: 0.8653 (mmt) REVERT: B 82 TYR cc_start: 0.7705 (p90) cc_final: 0.7477 (p90) REVERT: C 22 ASP cc_start: 0.8345 (m-30) cc_final: 0.7841 (t0) REVERT: C 224 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7226 (tm-30) REVERT: C 285 SER cc_start: 0.8990 (OUTLIER) cc_final: 0.8417 (t) REVERT: E 113 TYR cc_start: 0.8453 (t80) cc_final: 0.8005 (t80) REVERT: E 116 LEU cc_start: 0.8926 (pp) cc_final: 0.8707 (pp) REVERT: E 197 ASP cc_start: 0.6474 (p0) cc_final: 0.6206 (p0) REVERT: E 235 GLU cc_start: 0.8272 (pt0) cc_final: 0.7730 (pt0) REVERT: E 244 VAL cc_start: 0.8408 (m) cc_final: 0.8180 (t) outliers start: 56 outliers final: 39 residues processed: 240 average time/residue: 0.2101 time to fit residues: 78.1983 Evaluate side-chains 223 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 GLN 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 219 VAL 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 265 THR 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 197 LYS 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 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 81 VAL Chi-restraints excluded: chain E residue 108 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 228 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 126 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 138 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 41 optimal weight: 0.0670 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.124348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.101712 restraints weight = 21415.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.105192 restraints weight = 10850.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.107406 restraints weight = 7118.373| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14018 Z= 0.129 Angle : 0.618 9.781 19140 Z= 0.305 Chirality : 0.045 0.339 2215 Planarity : 0.003 0.051 2352 Dihedral : 6.864 96.406 2332 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.89 % Allowed : 22.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.21), residues: 1674 helix: 1.04 (0.23), residues: 558 sheet: -1.26 (0.27), residues: 383 loop : -2.40 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP D 246 HIS 0.002 0.000 HIS D 116 PHE 0.025 0.001 PHE C 249 TYR 0.015 0.001 TYR B 229 ARG 0.007 0.000 ARG D 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 9) link_NAG-ASN : angle 2.40955 ( 27) hydrogen bonds : bond 0.03327 ( 617) hydrogen bonds : angle 4.54894 ( 2016) SS BOND : bond 0.00223 ( 6) SS BOND : angle 1.77286 ( 12) covalent geometry : bond 0.00296 (14003) covalent geometry : angle 0.61080 (19101) *********************** 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: 56 poor density : 196 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8412 (mttt) cc_final: 0.8001 (ptmm) REVERT: A 117 ASP cc_start: 0.8276 (t0) cc_final: 0.7859 (t0) REVERT: A 154 MET cc_start: 0.7862 (mtm) cc_final: 0.7222 (mpp) REVERT: B 63 MET cc_start: 0.8874 (mmt) cc_final: 0.8622 (mmt) REVERT: B 82 TYR cc_start: 0.7717 (p90) cc_final: 0.7503 (p90) REVERT: C 22 ASP cc_start: 0.8331 (m-30) cc_final: 0.7866 (t0) REVERT: C 224 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7255 (tm-30) REVERT: C 285 SER cc_start: 0.8988 (OUTLIER) cc_final: 0.8582 (t) REVERT: C 286 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8640 (p90) REVERT: D 138 ARG cc_start: 0.9076 (ttt-90) cc_final: 0.8699 (ttt-90) REVERT: E 113 TYR cc_start: 0.8420 (t80) cc_final: 0.8007 (t80) REVERT: E 116 LEU cc_start: 0.8906 (pp) cc_final: 0.8679 (pp) REVERT: E 235 GLU cc_start: 0.8269 (pt0) cc_final: 0.7719 (pt0) REVERT: E 244 VAL cc_start: 0.8390 (m) cc_final: 0.8142 (t) outliers start: 56 outliers final: 41 residues processed: 240 average time/residue: 0.2367 time to fit residues: 85.5616 Evaluate side-chains 228 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 GLN 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 219 VAL Chi-restraints excluded: chain A residue 234 MET 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 102 LYS Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 197 LYS 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 287 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 108 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 228 THR 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 5 optimal weight: 5.9990 chunk 135 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** ** 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 = 0.3526 r_free = 0.3526 target = 0.125139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.102427 restraints weight = 21218.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.105978 restraints weight = 10834.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.108202 restraints weight = 7074.593| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14018 Z= 0.118 Angle : 0.619 10.435 19140 Z= 0.304 Chirality : 0.044 0.340 2215 Planarity : 0.003 0.051 2352 Dihedral : 6.747 94.674 2332 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.54 % Allowed : 23.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.21), residues: 1674 helix: 1.22 (0.23), residues: 558 sheet: -1.26 (0.26), residues: 411 loop : -2.35 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP D 246 HIS 0.002 0.000 HIS A 208 PHE 0.030 0.001 PHE A 249 TYR 0.014 0.001 TYR E 303 ARG 0.010 0.000 ARG B 259 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 9) link_NAG-ASN : angle 2.31852 ( 27) hydrogen bonds : bond 0.03232 ( 617) hydrogen bonds : angle 4.52798 ( 2016) SS BOND : bond 0.00235 ( 6) SS BOND : angle 2.88645 ( 12) covalent geometry : bond 0.00270 (14003) covalent geometry : angle 0.60871 (19101) *********************** 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 246 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 195 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8402 (mttt) cc_final: 0.7915 (ptmm) REVERT: A 117 ASP cc_start: 0.8215 (t0) cc_final: 0.7814 (t0) REVERT: A 154 MET cc_start: 0.7873 (mtm) cc_final: 0.7305 (mpp) REVERT: A 284 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8730 (p) REVERT: B 63 MET cc_start: 0.8836 (mmt) cc_final: 0.8505 (mmm) REVERT: C 22 ASP cc_start: 0.8282 (m-30) cc_final: 0.7845 (t0) REVERT: C 82 TYR cc_start: 0.8204 (p90) cc_final: 0.7749 (p90) REVERT: C 224 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7212 (tm-30) REVERT: C 285 SER cc_start: 0.8942 (OUTLIER) cc_final: 0.8412 (t) REVERT: D 117 ASP cc_start: 0.7821 (p0) cc_final: 0.7306 (p0) REVERT: E 113 TYR cc_start: 0.8388 (t80) cc_final: 0.7985 (t80) REVERT: E 116 LEU cc_start: 0.8876 (pp) cc_final: 0.8669 (pp) REVERT: E 235 GLU cc_start: 0.8283 (pt0) cc_final: 0.7748 (pt0) REVERT: E 244 VAL cc_start: 0.8295 (m) cc_final: 0.8072 (t) REVERT: E 291 CYS cc_start: 0.7962 (m) cc_final: 0.7588 (m) outliers start: 51 outliers final: 37 residues processed: 234 average time/residue: 0.2259 time to fit residues: 81.5357 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 : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 GLN 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 234 MET Chi-restraints excluded: chain A residue 284 VAL 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 211 THR 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 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 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 260 VAL 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 108 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 177 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 68 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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** ** 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 = 0.3517 r_free = 0.3517 target = 0.124352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.101859 restraints weight = 21265.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.105346 restraints weight = 10865.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.107537 restraints weight = 7114.645| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14018 Z= 0.145 Angle : 0.634 9.881 19140 Z= 0.313 Chirality : 0.045 0.339 2215 Planarity : 0.004 0.051 2352 Dihedral : 6.731 91.915 2332 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.26 % Allowed : 23.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.21), residues: 1674 helix: 1.15 (0.23), residues: 566 sheet: -1.19 (0.27), residues: 396 loop : -2.22 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP D 246 HIS 0.001 0.000 HIS E 132 PHE 0.026 0.001 PHE A 249 TYR 0.016 0.001 TYR B 229 ARG 0.009 0.000 ARG E 48 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 9) link_NAG-ASN : angle 2.34031 ( 27) hydrogen bonds : bond 0.03339 ( 617) hydrogen bonds : angle 4.54851 ( 2016) SS BOND : bond 0.00289 ( 6) SS BOND : angle 2.84899 ( 12) covalent geometry : bond 0.00341 (14003) covalent geometry : angle 0.62439 (19101) *********************** 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 239 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 1.574 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8409 (mttt) cc_final: 0.7927 (ptmm) REVERT: A 117 ASP cc_start: 0.8265 (t0) cc_final: 0.7841 (t0) REVERT: A 154 MET cc_start: 0.7866 (mtm) cc_final: 0.7224 (mpp) REVERT: A 284 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8838 (p) REVERT: B 63 MET cc_start: 0.8851 (mmt) cc_final: 0.8521 (mmm) REVERT: B 233 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7721 (tm-30) REVERT: C 22 ASP cc_start: 0.8303 (m-30) cc_final: 0.7832 (t0) REVERT: C 224 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7259 (tm-30) REVERT: C 285 SER cc_start: 0.9036 (OUTLIER) cc_final: 0.8597 (t) REVERT: C 286 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8647 (p90) REVERT: D 117 ASP cc_start: 0.7870 (p0) cc_final: 0.7357 (p0) REVERT: D 253 MET cc_start: 0.7792 (tpt) cc_final: 0.7496 (mmm) REVERT: E 113 TYR cc_start: 0.8418 (t80) cc_final: 0.8012 (t80) REVERT: E 116 LEU cc_start: 0.8889 (pp) cc_final: 0.8674 (pp) REVERT: E 235 GLU cc_start: 0.8273 (pt0) cc_final: 0.7701 (pt0) REVERT: E 244 VAL cc_start: 0.8399 (m) cc_final: 0.8134 (t) REVERT: E 291 CYS cc_start: 0.7956 (m) cc_final: 0.7577 (m) outliers start: 47 outliers final: 39 residues processed: 228 average time/residue: 0.2215 time to fit residues: 77.6157 Evaluate side-chains 228 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 GLN 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 234 MET Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 292 ILE 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 211 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 CYS 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 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 260 VAL 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 108 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 177 MET 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 107 optimal weight: 0.0170 chunk 8 optimal weight: 0.8980 chunk 146 optimal weight: 0.2980 chunk 30 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 overall best weight: 1.4422 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.124972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.102422 restraints weight = 21255.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.105897 restraints weight = 10896.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.108107 restraints weight = 7153.578| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14018 Z= 0.132 Angle : 0.634 10.127 19140 Z= 0.313 Chirality : 0.045 0.340 2215 Planarity : 0.003 0.052 2352 Dihedral : 6.643 89.430 2332 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.33 % Allowed : 24.22 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.21), residues: 1674 helix: 1.13 (0.23), residues: 568 sheet: -1.11 (0.27), residues: 396 loop : -2.16 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 246 HIS 0.002 0.000 HIS D 116 PHE 0.025 0.001 PHE A 249 TYR 0.017 0.001 TYR B 229 ARG 0.007 0.000 ARG B 259 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 9) link_NAG-ASN : angle 2.32019 ( 27) hydrogen bonds : bond 0.03291 ( 617) hydrogen bonds : angle 4.52544 ( 2016) SS BOND : bond 0.00238 ( 6) SS BOND : angle 2.71682 ( 12) covalent geometry : bond 0.00309 (14003) covalent geometry : angle 0.62468 (19101) ********************** 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 242 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: A 40 LYS cc_start: 0.8409 (mttt) cc_final: 0.7940 (ptmm) REVERT: A 117 ASP cc_start: 0.8173 (t0) cc_final: 0.7795 (t0) REVERT: A 154 MET cc_start: 0.7878 (mtm) cc_final: 0.7228 (mpp) REVERT: A 284 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8723 (p) REVERT: B 63 MET cc_start: 0.8834 (mmt) cc_final: 0.8535 (mmm) REVERT: B 233 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7787 (tm-30) REVERT: C 22 ASP cc_start: 0.8295 (m-30) cc_final: 0.7834 (t0) REVERT: C 224 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7260 (tm-30) REVERT: C 285 SER cc_start: 0.8996 (OUTLIER) cc_final: 0.8599 (t) REVERT: D 117 ASP cc_start: 0.7877 (p0) cc_final: 0.7376 (p0) REVERT: D 193 GLN cc_start: 0.8208 (tt0) cc_final: 0.7676 (pm20) REVERT: D 241 ILE cc_start: 0.8284 (mm) cc_final: 0.8003 (mm) REVERT: D 249 PHE cc_start: 0.8223 (p90) cc_final: 0.7959 (p90) REVERT: D 253 MET cc_start: 0.7769 (tpt) cc_final: 0.7384 (mmm) REVERT: E 113 TYR cc_start: 0.8411 (t80) cc_final: 0.8009 (t80) REVERT: E 116 LEU cc_start: 0.8877 (pp) cc_final: 0.8665 (pp) REVERT: E 235 GLU cc_start: 0.8270 (pt0) cc_final: 0.7715 (pt0) REVERT: E 244 VAL cc_start: 0.8378 (m) cc_final: 0.8108 (t) REVERT: E 291 CYS cc_start: 0.7927 (m) cc_final: 0.7562 (m) outliers start: 48 outliers final: 42 residues processed: 230 average time/residue: 0.2145 time to fit residues: 76.1239 Evaluate side-chains 238 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 74 GLN 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 234 MET Chi-restraints excluded: chain A residue 284 VAL 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 211 THR 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 268 LEU Chi-restraints excluded: chain C residue 105 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 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 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 81 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 301 VAL 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 128 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 116 optimal weight: 0.0050 chunk 121 optimal weight: 3.9990 overall best weight: 1.9400 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.123928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.101358 restraints weight = 21503.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.104815 restraints weight = 10969.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106996 restraints weight = 7200.522| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14018 Z= 0.153 Angle : 0.643 10.534 19140 Z= 0.318 Chirality : 0.045 0.339 2215 Planarity : 0.004 0.051 2352 Dihedral : 6.623 85.835 2332 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.33 % Allowed : 24.15 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1674 helix: 1.07 (0.22), residues: 572 sheet: -1.14 (0.27), residues: 396 loop : -2.13 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 246 HIS 0.002 0.000 HIS E 132 PHE 0.025 0.001 PHE A 249 TYR 0.019 0.001 TYR B 229 ARG 0.005 0.000 ARG D 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 9) link_NAG-ASN : angle 2.39382 ( 27) hydrogen bonds : bond 0.03371 ( 617) hydrogen bonds : angle 4.57645 ( 2016) SS BOND : bond 0.00350 ( 6) SS BOND : angle 2.89445 ( 12) covalent geometry : bond 0.00360 (14003) covalent geometry : angle 0.63358 (19101) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3898.19 seconds wall clock time: 68 minutes 44.10 seconds (4124.10 seconds total)