Starting phenix.real_space_refine on Fri Sep 27 23:29:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3v_22034/09_2024/6x3v_22034.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3v_22034/09_2024/6x3v_22034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3v_22034/09_2024/6x3v_22034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3v_22034/09_2024/6x3v_22034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3v_22034/09_2024/6x3v_22034.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3v_22034/09_2024/6x3v_22034.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 97 5.16 5 C 11253 2.51 5 N 2833 2.21 5 O 3243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17426 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2729 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'ABU': 1, 'NAG': 1, 'V8D': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'ABU': 1, 'NAG': 1, 'V8D': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.73, per 1000 atoms: 0.62 Number of scatterers: 17426 At special positions: 0 Unit cell: (135.779, 121.618, 129.948, 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 97 16.00 O 3243 8.00 N 2833 7.00 C 11253 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 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 ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 10 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 404 " - " ASN A 80 " " NAG C 404 " - " ASN C 80 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN D 111 " " NAG N 1 " - " ASN E 208 " Time building additional restraints: 4.96 Conformation dependent library (CDL) restraints added in 2.2 seconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 32 sheets defined 31.4% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.552A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 226 through 238 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 246 through 270 removed outlier: 3.954A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 309 through 340 removed outlier: 3.969A pdb=" N ALA A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 11 through 23 Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.654A pdb=" N LYS B 76 " --> pdb=" O GLU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 230 removed outlier: 3.526A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 243 Processing helix chain 'B' and resid 244 through 247 removed outlier: 3.560A pdb=" N LEU B 247 " --> pdb=" O SER B 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 244 through 247' Processing helix chain 'B' and resid 251 through 275 removed outlier: 3.665A pdb=" N ARG B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 311 removed outlier: 3.597A pdb=" N TRP B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 346 removed outlier: 3.938A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix removed outlier: 3.609A pdb=" N ASN B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.549A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 225 through 238 removed outlier: 3.763A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 248 through 270 Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 309 through 339 removed outlier: 3.549A pdb=" N ALA C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 11 through 24 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.589A pdb=" N SER D 92 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 243 removed outlier: 4.319A pdb=" N LEU D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 251 through 277 removed outlier: 3.871A pdb=" N ARG D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 311 Processing helix chain 'D' and resid 314 through 346 removed outlier: 4.151A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.803A pdb=" N LYS E 105 " --> pdb=" O MET E 102 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE E 106 " --> pdb=" O VAL E 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 102 through 106' Processing helix chain 'E' and resid 234 through 253 removed outlier: 4.426A pdb=" N ILE E 238 " --> pdb=" O GLY E 234 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 261 through 287 removed outlier: 3.701A pdb=" N ARG E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU E 287 " --> pdb=" O ALA E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 324 removed outlier: 3.584A pdb=" N PHE E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 356 removed outlier: 3.843A pdb=" N ALA E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) Proline residue: E 340 - end of helix Processing helix chain 'J' and resid 87 through 91 removed outlier: 4.140A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.701A pdb=" N GLN K 65 " --> pdb=" O PRO K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.740A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 132 removed outlier: 6.922A pdb=" N ASP A 56 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL A 50 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR A 58 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.845A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 54 removed outlier: 4.649A pdb=" N THR B 61 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL B 53 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLU B 59 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 46 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 86 removed outlier: 4.200A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 46 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N VAL B 180 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 45 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.063A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.063A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N TYR B 210 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE B 202 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 212 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER B 200 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR B 214 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL B 198 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS B 216 " --> pdb=" O GLN B 196 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN B 196 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N HIS B 218 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.642A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.642A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N THR C 176 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE C 42 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.829A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.829A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL C 199 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR C 205 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS C 197 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG C 207 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR C 195 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER C 209 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU C 193 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER C 211 " --> pdb=" O TYR C 191 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TYR C 191 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS C 213 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 39 through 43 removed outlier: 6.062A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 84 through 86 removed outlier: 4.338A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR D 130 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 108 " --> pdb=" O THR D 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 84 through 86 removed outlier: 4.338A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR D 130 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER D 49 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE D 65 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL D 47 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG D 67 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ILE D 45 " --> pdb=" O ARG D 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.995A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.995A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 61 through 66 removed outlier: 3.705A pdb=" N SER E 61 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR E 73 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL E 65 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU E 71 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ARG E 144 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA E 121 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.595A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS E 184 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N MET E 57 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N SER E 186 " --> pdb=" O MET E 57 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.541A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.540A pdb=" N THR I 101 " --> pdb=" O TYR I 86 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR I 86 " --> pdb=" O THR I 101 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.540A pdb=" N THR I 101 " --> pdb=" O TYR I 86 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR I 86 " --> pdb=" O THR I 101 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN I 90 " --> pdb=" O THR I 96 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR I 96 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.161A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.161A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR J 107 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.541A pdb=" N MET L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.422A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.596A pdb=" N VAL K 18 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.707A pdb=" N GLU K 10 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR K 94 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.707A pdb=" N GLU K 10 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR K 94 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 814 hydrogen bonds defined for protein. 2325 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.59 Time building geometry restraints manager: 5.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2670 1.31 - 1.43: 5257 1.43 - 1.56: 9767 1.56 - 1.69: 1 1.69 - 1.82: 167 Bond restraints: 17862 Sorted by residual: bond pdb=" C13 V8D A 406 " pdb=" O02 V8D A 406 " ideal model delta sigma weight residual 1.209 1.398 -0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" C13 V8D C 406 " pdb=" O02 V8D C 406 " ideal model delta sigma weight residual 1.209 1.397 -0.188 2.00e-02 2.50e+03 8.86e+01 bond pdb=" C13 V8D C 406 " pdb=" O01 V8D C 406 " ideal model delta sigma weight residual 1.325 1.180 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" C13 V8D A 406 " pdb=" O01 V8D A 406 " ideal model delta sigma weight residual 1.325 1.182 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" C08 V8D C 406 " pdb=" C13 V8D C 406 " ideal model delta sigma weight residual 1.459 1.530 -0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 17857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 23859 1.99 - 3.98: 347 3.98 - 5.98: 67 5.98 - 7.97: 12 7.97 - 9.96: 3 Bond angle restraints: 24288 Sorted by residual: angle pdb=" C08 V8D A 406 " pdb=" C13 V8D A 406 " pdb=" O01 V8D A 406 " ideal model delta sigma weight residual 110.46 120.42 -9.96 3.00e+00 1.11e-01 1.10e+01 angle pdb=" N GLY K 56 " pdb=" CA GLY K 56 " pdb=" C GLY K 56 " ideal model delta sigma weight residual 115.63 110.77 4.86 1.49e+00 4.50e-01 1.07e+01 angle pdb=" C08 V8D C 406 " pdb=" C13 V8D C 406 " pdb=" O01 V8D C 406 " ideal model delta sigma weight residual 110.46 120.24 -9.78 3.00e+00 1.11e-01 1.06e+01 angle pdb=" N MET B 114 " pdb=" CA MET B 114 " pdb=" C MET B 114 " ideal model delta sigma weight residual 110.13 106.39 3.74 1.15e+00 7.56e-01 1.06e+01 angle pdb=" N ALA B 161 " pdb=" CA ALA B 161 " pdb=" CB ALA B 161 " ideal model delta sigma weight residual 114.17 110.83 3.34 1.14e+00 7.69e-01 8.56e+00 ... (remaining 24283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 10032 21.78 - 43.56: 681 43.56 - 65.34: 70 65.34 - 87.12: 32 87.12 - 108.90: 17 Dihedral angle restraints: 10832 sinusoidal: 4576 harmonic: 6256 Sorted by residual: dihedral pdb=" CB CYS A 136 " pdb=" SG CYS A 136 " pdb=" SG CYS A 150 " pdb=" CB CYS A 150 " ideal model delta sinusoidal sigma weight residual -86.00 -24.88 -61.12 1 1.00e+01 1.00e-02 4.96e+01 dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual -86.00 -31.80 -54.20 1 1.00e+01 1.00e-02 3.98e+01 dihedral pdb=" CA CYS A 150 " pdb=" C CYS A 150 " pdb=" N THR A 151 " pdb=" CA THR A 151 " ideal model delta harmonic sigma weight residual -180.00 -152.15 -27.85 0 5.00e+00 4.00e-02 3.10e+01 ... (remaining 10829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2372 0.060 - 0.121: 406 0.121 - 0.181: 24 0.181 - 0.241: 4 0.241 - 0.302: 3 Chirality restraints: 2809 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN D 111 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.98e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 2806 not shown) Planarity restraints: 2995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 227 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C VAL D 227 " 0.047 2.00e-02 2.50e+03 pdb=" O VAL D 227 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE D 228 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 227 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" C VAL B 227 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL B 227 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE B 228 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 277 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO D 278 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 278 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 278 " -0.022 5.00e-02 4.00e+02 ... (remaining 2992 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 413 2.69 - 3.24: 16500 3.24 - 3.79: 26585 3.79 - 4.35: 36158 4.35 - 4.90: 61897 Nonbonded interactions: 141553 Sorted by model distance: nonbonded pdb=" OG1 THR B 99 " pdb=" OH TYR B 169 " model vdw 2.136 3.040 nonbonded pdb=" OG1 THR E 111 " pdb=" OH TYR E 181 " model vdw 2.144 3.040 nonbonded pdb=" NE2 HIS C 107 " pdb=" OG1 THR C 131 " model vdw 2.194 3.120 nonbonded pdb=" OG1 THR D 99 " pdb=" OH TYR D 169 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR L 63 " pdb=" OG1 THR L 74 " model vdw 2.213 3.040 ... (remaining 141548 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 41.000 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 0.189 17862 Z= 0.368 Angle : 0.653 9.958 24288 Z= 0.340 Chirality : 0.046 0.302 2809 Planarity : 0.004 0.040 2988 Dihedral : 15.050 108.897 6785 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.58 % Allowed : 10.67 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -2.83 (0.16), residues: 2103 helix: 0.10 (0.19), residues: 564 sheet: -2.64 (0.17), residues: 675 loop : -2.46 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 67 HIS 0.004 0.001 HIS C 267 PHE 0.014 0.001 PHE D 226 TYR 0.016 0.002 TYR C 299 ARG 0.002 0.000 ARG B 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 284 time to evaluate : 1.944 Fit side-chains REVERT: A 99 LEU cc_start: 0.9129 (tp) cc_final: 0.8923 (tp) REVERT: A 283 MET cc_start: 0.7392 (tpp) cc_final: 0.7122 (tpp) REVERT: A 304 TYR cc_start: 0.8540 (t80) cc_final: 0.8227 (t80) REVERT: B 308 ASN cc_start: 0.8642 (t0) cc_final: 0.8324 (t0) REVERT: C 321 ARG cc_start: 0.8278 (mtm180) cc_final: 0.7856 (mtt180) REVERT: D 58 MET cc_start: 0.8000 (mtt) cc_final: 0.7710 (mtm) REVERT: D 323 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7660 (ttp80) REVERT: E 338 PHE cc_start: 0.7538 (t80) cc_final: 0.7291 (t80) REVERT: I 11 MET cc_start: 0.7911 (ppp) cc_final: 0.7696 (ppp) REVERT: L 106 LYS cc_start: 0.5232 (tptt) cc_final: 0.5031 (tptt) outliers start: 11 outliers final: 7 residues processed: 295 average time/residue: 0.3613 time to fit residues: 151.6330 Evaluate side-chains 249 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 242 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 187 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 90 GLN B 102 HIS ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN E 90 ASN E 324 GLN E 347 ASN K 5 GLN ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17862 Z= 0.185 Angle : 0.540 7.588 24288 Z= 0.277 Chirality : 0.043 0.189 2809 Planarity : 0.004 0.041 2988 Dihedral : 8.875 74.516 2852 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.28 % Allowed : 13.49 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -1.64 (0.18), residues: 2103 helix: 1.55 (0.21), residues: 563 sheet: -2.23 (0.18), residues: 690 loop : -1.81 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 67 HIS 0.004 0.001 HIS C 267 PHE 0.012 0.001 PHE B 146 TYR 0.027 0.001 TYR L 49 ARG 0.002 0.000 ARG D 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 246 time to evaluate : 2.586 Fit side-chains REVERT: A 283 MET cc_start: 0.7438 (tpp) cc_final: 0.7180 (tpp) REVERT: A 304 TYR cc_start: 0.8605 (t80) cc_final: 0.8286 (t80) REVERT: B 308 ASN cc_start: 0.8644 (t0) cc_final: 0.8391 (t0) REVERT: C 265 ASN cc_start: 0.8738 (t0) cc_final: 0.8375 (t0) REVERT: C 321 ARG cc_start: 0.8219 (mtm180) cc_final: 0.7803 (mtt180) REVERT: D 323 ARG cc_start: 0.7910 (ttp80) cc_final: 0.7703 (ttp80) REVERT: E 223 MET cc_start: 0.7931 (mmm) cc_final: 0.7408 (mmm) REVERT: E 338 PHE cc_start: 0.7554 (t80) cc_final: 0.7326 (t80) REVERT: I 45 LYS cc_start: 0.8689 (mmmt) cc_final: 0.8386 (mtpt) outliers start: 43 outliers final: 31 residues processed: 274 average time/residue: 0.3240 time to fit residues: 130.6575 Evaluate side-chains 260 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 229 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 203 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 275 ASN D 116 ASN ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17862 Z= 0.268 Angle : 0.551 10.427 24288 Z= 0.281 Chirality : 0.044 0.193 2809 Planarity : 0.004 0.040 2988 Dihedral : 7.287 63.350 2851 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.24 % Allowed : 14.60 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.18), residues: 2103 helix: 1.99 (0.21), residues: 563 sheet: -1.90 (0.18), residues: 681 loop : -1.54 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 67 HIS 0.002 0.001 HIS C 267 PHE 0.014 0.001 PHE B 146 TYR 0.031 0.001 TYR L 49 ARG 0.005 0.000 ARG E 327 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 246 time to evaluate : 1.915 Fit side-chains REVERT: A 9 MET cc_start: 0.8215 (tpp) cc_final: 0.7899 (tpp) REVERT: A 283 MET cc_start: 0.7539 (tpp) cc_final: 0.7227 (tpp) REVERT: A 304 TYR cc_start: 0.8620 (t80) cc_final: 0.8262 (t80) REVERT: B 308 ASN cc_start: 0.8681 (t0) cc_final: 0.8147 (t0) REVERT: C 164 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9266 (tt) REVERT: C 265 ASN cc_start: 0.8783 (t0) cc_final: 0.8458 (t0) REVERT: C 321 ARG cc_start: 0.8281 (mtm180) cc_final: 0.7837 (mtt180) REVERT: D 338 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7156 (mp) REVERT: E 223 MET cc_start: 0.8000 (mmm) cc_final: 0.7460 (mmm) REVERT: E 311 LEU cc_start: 0.8923 (tp) cc_final: 0.8718 (tp) REVERT: E 338 PHE cc_start: 0.7559 (t80) cc_final: 0.7329 (t80) REVERT: I 45 LYS cc_start: 0.8653 (mmmt) cc_final: 0.8361 (mtpt) outliers start: 61 outliers final: 46 residues processed: 283 average time/residue: 0.3025 time to fit residues: 126.9117 Evaluate side-chains 281 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 233 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 0.0170 chunk 126 optimal weight: 0.4980 chunk 188 optimal weight: 0.9990 chunk 200 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 179 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN L 79 GLN ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17862 Z= 0.170 Angle : 0.512 9.129 24288 Z= 0.259 Chirality : 0.043 0.193 2809 Planarity : 0.003 0.040 2988 Dihedral : 6.374 55.357 2850 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.35 % Allowed : 15.51 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.70 (0.19), residues: 2103 helix: 2.35 (0.21), residues: 563 sheet: -1.66 (0.19), residues: 691 loop : -1.26 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 103 HIS 0.003 0.001 HIS C 267 PHE 0.017 0.001 PHE E 158 TYR 0.031 0.001 TYR L 49 ARG 0.004 0.000 ARG E 327 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 252 time to evaluate : 2.117 Fit side-chains REVERT: A 9 MET cc_start: 0.8256 (tpp) cc_final: 0.7992 (tpp) REVERT: A 283 MET cc_start: 0.7443 (tpp) cc_final: 0.7190 (tpp) REVERT: A 304 TYR cc_start: 0.8621 (t80) cc_final: 0.8231 (t80) REVERT: B 308 ASN cc_start: 0.8624 (t0) cc_final: 0.8098 (t0) REVERT: C 265 ASN cc_start: 0.8731 (t0) cc_final: 0.8434 (t0) REVERT: C 321 ARG cc_start: 0.8220 (mtm180) cc_final: 0.7756 (mtt180) REVERT: E 223 MET cc_start: 0.7967 (mmm) cc_final: 0.7419 (mmm) REVERT: E 338 PHE cc_start: 0.7569 (t80) cc_final: 0.7328 (t80) REVERT: I 45 LYS cc_start: 0.8599 (mmmt) cc_final: 0.8330 (mtpt) REVERT: J 90 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7880 (t0) REVERT: K 91 THR cc_start: 0.8066 (p) cc_final: 0.7744 (t) outliers start: 63 outliers final: 48 residues processed: 292 average time/residue: 0.3057 time to fit residues: 132.4535 Evaluate side-chains 291 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 242 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.0980 chunk 113 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 179 optimal weight: 9.9990 chunk 50 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN B 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17862 Z= 0.135 Angle : 0.491 8.318 24288 Z= 0.247 Chirality : 0.042 0.185 2809 Planarity : 0.003 0.042 2988 Dihedral : 5.796 57.141 2850 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.13 % Allowed : 16.57 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.36 (0.19), residues: 2103 helix: 2.58 (0.21), residues: 565 sheet: -1.40 (0.19), residues: 683 loop : -1.09 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 237 HIS 0.003 0.000 HIS C 267 PHE 0.015 0.001 PHE E 158 TYR 0.033 0.001 TYR L 49 ARG 0.005 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 247 time to evaluate : 2.158 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.8261 (tpp) cc_final: 0.8005 (tpp) REVERT: A 132 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8393 (p) REVERT: B 308 ASN cc_start: 0.8484 (t0) cc_final: 0.8067 (t0) REVERT: C 321 ARG cc_start: 0.8143 (mtm180) cc_final: 0.7669 (mtt180) REVERT: D 324 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8752 (mp) REVERT: D 338 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7069 (mp) REVERT: E 223 MET cc_start: 0.7962 (mmm) cc_final: 0.7380 (mmm) REVERT: E 338 PHE cc_start: 0.7581 (t80) cc_final: 0.7341 (t80) REVERT: I 45 LYS cc_start: 0.8599 (mmmt) cc_final: 0.8320 (mtpt) REVERT: J 90 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7828 (t0) outliers start: 59 outliers final: 45 residues processed: 286 average time/residue: 0.3001 time to fit residues: 128.2655 Evaluate side-chains 283 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 234 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17862 Z= 0.196 Angle : 0.512 7.884 24288 Z= 0.258 Chirality : 0.043 0.194 2809 Planarity : 0.003 0.042 2988 Dihedral : 5.672 59.790 2850 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.40 % Allowed : 17.58 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.28 (0.19), residues: 2103 helix: 2.60 (0.21), residues: 565 sheet: -1.39 (0.19), residues: 691 loop : -0.97 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 103 HIS 0.003 0.001 HIS C 267 PHE 0.013 0.001 PHE E 158 TYR 0.033 0.001 TYR L 49 ARG 0.005 0.000 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 245 time to evaluate : 1.836 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.8269 (tpp) cc_final: 0.7975 (tpp) REVERT: B 242 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7515 (mt0) REVERT: B 308 ASN cc_start: 0.8473 (t0) cc_final: 0.8079 (t0) REVERT: C 265 ASN cc_start: 0.8742 (t0) cc_final: 0.8459 (t0) REVERT: C 321 ARG cc_start: 0.8153 (mtm180) cc_final: 0.7661 (mtt180) REVERT: E 223 MET cc_start: 0.7984 (mmm) cc_final: 0.7409 (mmm) REVERT: E 338 PHE cc_start: 0.7544 (t80) cc_final: 0.7312 (t80) REVERT: I 45 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8308 (mtpt) outliers start: 64 outliers final: 54 residues processed: 286 average time/residue: 0.3314 time to fit residues: 140.4713 Evaluate side-chains 297 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 242 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 146 optimal weight: 0.0770 chunk 113 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 92 optimal weight: 0.0980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17862 Z= 0.142 Angle : 0.497 7.640 24288 Z= 0.249 Chirality : 0.042 0.171 2809 Planarity : 0.003 0.043 2988 Dihedral : 5.564 57.041 2850 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.29 % Allowed : 17.79 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.12 (0.19), residues: 2103 helix: 2.71 (0.21), residues: 565 sheet: -1.29 (0.19), residues: 695 loop : -0.86 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 103 HIS 0.003 0.000 HIS C 267 PHE 0.012 0.001 PHE E 158 TYR 0.033 0.001 TYR L 49 ARG 0.004 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 249 time to evaluate : 1.948 Fit side-chains revert: symmetry clash REVERT: A 9 MET cc_start: 0.8238 (tpp) cc_final: 0.8000 (tpp) REVERT: A 132 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8418 (p) REVERT: B 242 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7492 (mt0) REVERT: B 308 ASN cc_start: 0.8398 (t0) cc_final: 0.8004 (t0) REVERT: C 321 ARG cc_start: 0.8134 (mtm180) cc_final: 0.7617 (mtt180) REVERT: E 223 MET cc_start: 0.7950 (mmm) cc_final: 0.7384 (mmm) REVERT: E 338 PHE cc_start: 0.7585 (t80) cc_final: 0.7329 (t80) REVERT: I 45 LYS cc_start: 0.8544 (mmmt) cc_final: 0.8263 (mtpt) outliers start: 62 outliers final: 51 residues processed: 291 average time/residue: 0.2992 time to fit residues: 129.9945 Evaluate side-chains 293 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 240 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 156 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17862 Z= 0.200 Angle : 0.522 7.473 24288 Z= 0.261 Chirality : 0.043 0.183 2809 Planarity : 0.003 0.043 2988 Dihedral : 5.519 53.216 2850 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.51 % Allowed : 17.74 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.10 (0.19), residues: 2103 helix: 2.71 (0.21), residues: 565 sheet: -1.27 (0.19), residues: 677 loop : -0.86 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 103 HIS 0.003 0.001 HIS C 267 PHE 0.012 0.001 PHE C 306 TYR 0.035 0.001 TYR L 49 ARG 0.004 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 243 time to evaluate : 1.958 Fit side-chains revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8384 (mt) REVERT: B 242 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: B 308 ASN cc_start: 0.8447 (t0) cc_final: 0.8063 (t0) REVERT: C 321 ARG cc_start: 0.8151 (mtm180) cc_final: 0.7634 (mtt180) REVERT: E 223 MET cc_start: 0.7989 (mmm) cc_final: 0.7423 (mmm) REVERT: E 338 PHE cc_start: 0.7594 (t80) cc_final: 0.7358 (t80) REVERT: I 11 MET cc_start: 0.7330 (ppp) cc_final: 0.6823 (ppp) REVERT: I 45 LYS cc_start: 0.8519 (mmmt) cc_final: 0.8265 (mtpt) outliers start: 66 outliers final: 55 residues processed: 288 average time/residue: 0.3025 time to fit residues: 130.2792 Evaluate side-chains 296 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 239 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 145 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 175 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17862 Z= 0.184 Angle : 0.521 8.090 24288 Z= 0.260 Chirality : 0.043 0.187 2809 Planarity : 0.003 0.040 2988 Dihedral : 5.473 53.046 2850 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.13 % Allowed : 18.32 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.04 (0.19), residues: 2103 helix: 2.73 (0.21), residues: 565 sheet: -1.23 (0.19), residues: 677 loop : -0.81 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 108 HIS 0.002 0.000 HIS D 110 PHE 0.013 0.001 PHE C 306 TYR 0.034 0.001 TYR L 49 ARG 0.007 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 247 time to evaluate : 1.905 Fit side-chains revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8386 (mt) REVERT: B 308 ASN cc_start: 0.8427 (t0) cc_final: 0.8055 (t0) REVERT: C 321 ARG cc_start: 0.8136 (mtm180) cc_final: 0.7743 (mtt180) REVERT: E 223 MET cc_start: 0.7980 (mmm) cc_final: 0.7408 (mmm) REVERT: E 338 PHE cc_start: 0.7595 (t80) cc_final: 0.7352 (t80) REVERT: I 45 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8266 (mtpt) REVERT: K 3 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7481 (tp40) outliers start: 59 outliers final: 55 residues processed: 287 average time/residue: 0.3106 time to fit residues: 132.7927 Evaluate side-chains 296 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 239 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 136 optimal weight: 0.0770 chunk 206 optimal weight: 0.8980 chunk 189 optimal weight: 0.6980 chunk 164 optimal weight: 0.0980 chunk 17 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 242 GLN D 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 17862 Z= 0.142 Angle : 0.510 8.692 24288 Z= 0.254 Chirality : 0.042 0.178 2809 Planarity : 0.003 0.042 2988 Dihedral : 5.346 53.731 2850 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.92 % Allowed : 18.91 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.09 (0.19), residues: 2103 helix: 2.81 (0.21), residues: 565 sheet: -1.13 (0.19), residues: 671 loop : -0.72 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 237 HIS 0.003 0.000 HIS C 267 PHE 0.016 0.001 PHE C 306 TYR 0.033 0.001 TYR L 49 ARG 0.007 0.000 ARG L 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 241 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8358 (mt) REVERT: B 308 ASN cc_start: 0.8353 (t0) cc_final: 0.8014 (t0) REVERT: E 223 MET cc_start: 0.7931 (mmm) cc_final: 0.7358 (mmm) REVERT: E 338 PHE cc_start: 0.7603 (t80) cc_final: 0.7357 (t80) REVERT: I 11 MET cc_start: 0.7202 (ppp) cc_final: 0.6748 (ppp) REVERT: I 45 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8284 (mtpt) REVERT: J 34 MET cc_start: 0.8324 (tpp) cc_final: 0.7986 (mmt) REVERT: K 3 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7468 (tp40) outliers start: 55 outliers final: 48 residues processed: 279 average time/residue: 0.3131 time to fit residues: 130.2888 Evaluate side-chains 288 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 238 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 1.9990 chunk 50 optimal weight: 0.0270 chunk 151 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 68 optimal weight: 0.0470 chunk 168 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.126190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.101724 restraints weight = 21516.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.103625 restraints weight = 15380.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.104916 restraints weight = 12304.456| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 17862 Z= 0.143 Angle : 0.514 8.436 24288 Z= 0.255 Chirality : 0.042 0.178 2809 Planarity : 0.003 0.042 2988 Dihedral : 5.274 57.018 2850 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.55 % Allowed : 19.38 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.21 (0.19), residues: 2103 helix: 2.84 (0.21), residues: 565 sheet: -0.99 (0.19), residues: 681 loop : -0.65 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 241 HIS 0.003 0.000 HIS C 267 PHE 0.018 0.001 PHE C 306 TYR 0.035 0.001 TYR L 49 ARG 0.007 0.000 ARG L 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3690.26 seconds wall clock time: 67 minutes 8.60 seconds (4028.60 seconds total)