Starting phenix.real_space_refine on Thu Jan 15 07:03:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z6s_14529/01_2026/7z6s_14529.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z6s_14529/01_2026/7z6s_14529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z6s_14529/01_2026/7z6s_14529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z6s_14529/01_2026/7z6s_14529.map" model { file = "/net/cci-nas-00/data/ceres_data/7z6s_14529/01_2026/7z6s_14529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z6s_14529/01_2026/7z6s_14529.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5434 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 10 5.49 5 Mg 2 5.21 5 S 122 5.16 5 C 12046 2.51 5 N 3334 2.21 5 O 3618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19134 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3418 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Chain: "B" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2722 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2722 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 317} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.17, per 1000 atoms: 0.27 Number of scatterers: 19134 At special positions: 0 Unit cell: (118.3, 100.1, 201.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 122 16.00 P 10 15.00 Mg 2 11.99 O 3618 8.00 N 3334 7.00 C 12046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Links applied TRANS " VAL K 440 " - " ARG C 259 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 826.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 280 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 285 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 280 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 285 " 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4456 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 14 sheets defined 56.6% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.660A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.670A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.735A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.652A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.877A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.039A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.611A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.979A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 79 removed outlier: 4.430A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.547A pdb=" N PHE B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 127 removed outlier: 3.860A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.518A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.575A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.701A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.633A pdb=" N ASN B 337 " --> pdb=" O ILE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 374 through 391 removed outlier: 3.632A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.062A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.865A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 29 Processing helix chain 'H' and resid 40 through 46 removed outlier: 4.179A pdb=" N LEU H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG H 46 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 69 through 79 removed outlier: 4.429A pdb=" N MET H 73 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.546A pdb=" N PHE H 90 " --> pdb=" O PRO H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 108 through 127 removed outlier: 3.860A pdb=" N LEU H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 159 Processing helix chain 'H' and resid 180 through 196 removed outlier: 3.518A pdb=" N ASN H 184 " --> pdb=" O VAL H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 213 Processing helix chain 'H' and resid 221 through 242 removed outlier: 3.575A pdb=" N LEU H 225 " --> pdb=" O THR H 221 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU H 240 " --> pdb=" O VAL H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 258 Processing helix chain 'H' and resid 285 through 294 removed outlier: 3.700A pdb=" N PHE H 294 " --> pdb=" O THR H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 299 Processing helix chain 'H' and resid 304 through 308 Processing helix chain 'H' and resid 322 through 337 removed outlier: 3.634A pdb=" N ASN H 337 " --> pdb=" O ILE H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 341 Processing helix chain 'H' and resid 374 through 391 removed outlier: 3.633A pdb=" N ARG H 391 " --> pdb=" O ALA H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 400 removed outlier: 4.063A pdb=" N TYR H 398 " --> pdb=" O PHE H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 427 removed outlier: 3.866A pdb=" N PHE H 408 " --> pdb=" O ASP H 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 28 Processing helix chain 'K' and resid 48 through 51 Processing helix chain 'K' and resid 71 through 81 removed outlier: 4.659A pdb=" N ILE K 75 " --> pdb=" O GLU K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 110 through 113 Processing helix chain 'K' and resid 114 through 128 Processing helix chain 'K' and resid 143 through 161 Processing helix chain 'K' and resid 182 through 195 Processing helix chain 'K' and resid 205 through 216 removed outlier: 3.669A pdb=" N ILE K 209 " --> pdb=" O ASP K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 244 removed outlier: 3.734A pdb=" N LEU K 227 " --> pdb=" O THR K 223 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 260 removed outlier: 3.653A pdb=" N VAL K 260 " --> pdb=" O GLN K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 297 Processing helix chain 'K' and resid 306 through 310 Processing helix chain 'K' and resid 324 through 338 Processing helix chain 'K' and resid 383 through 401 removed outlier: 3.878A pdb=" N ALA K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 411 removed outlier: 4.040A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.611A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL K 437 " --> pdb=" O GLU K 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 158 Processing helix chain 'C' and resid 173 through 180 Processing helix chain 'C' and resid 187 through 203 Processing helix chain 'C' and resid 204 through 214 removed outlier: 3.663A pdb=" N GLY C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 234 Processing helix chain 'C' and resid 270 through 282 removed outlier: 4.152A pdb=" N GLU C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 294 removed outlier: 3.698A pdb=" N ARG C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 307 Processing helix chain 'C' and resid 313 through 324 removed outlier: 3.669A pdb=" N VAL C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 346 Processing helix chain 'C' and resid 349 through 357 Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 363 through 375 Processing helix chain 'C' and resid 387 through 390 removed outlier: 4.509A pdb=" N ASP C 390 " --> pdb=" O PHE C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 387 through 390' Processing helix chain 'C' and resid 391 through 403 Processing helix chain 'C' and resid 408 through 415 Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' Processing helix chain 'C' and resid 422 through 427 Processing helix chain 'C' and resid 428 through 430 No H-bonds generated for 'chain 'C' and resid 428 through 430' Processing helix chain 'C' and resid 438 through 442 Processing helix chain 'C' and resid 443 through 458 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'E' and resid 147 through 158 Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'E' and resid 187 through 203 Processing helix chain 'E' and resid 204 through 214 removed outlier: 3.664A pdb=" N GLY E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 234 Processing helix chain 'E' and resid 270 through 282 removed outlier: 4.153A pdb=" N GLU E 275 " --> pdb=" O GLN E 271 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY E 276 " --> pdb=" O TYR E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 294 removed outlier: 3.698A pdb=" N ARG E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 307 Processing helix chain 'E' and resid 313 through 324 removed outlier: 3.669A pdb=" N VAL E 324 " --> pdb=" O SER E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 346 Processing helix chain 'E' and resid 349 through 357 Processing helix chain 'E' and resid 358 through 360 No H-bonds generated for 'chain 'E' and resid 358 through 360' Processing helix chain 'E' and resid 363 through 375 Processing helix chain 'E' and resid 387 through 390 removed outlier: 4.509A pdb=" N ASP E 390 " --> pdb=" O PHE E 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 387 through 390' Processing helix chain 'E' and resid 391 through 403 Processing helix chain 'E' and resid 408 through 415 Processing helix chain 'E' and resid 419 through 421 No H-bonds generated for 'chain 'E' and resid 419 through 421' Processing helix chain 'E' and resid 422 through 427 Processing helix chain 'E' and resid 428 through 430 No H-bonds generated for 'chain 'E' and resid 428 through 430' Processing helix chain 'E' and resid 438 through 442 Processing helix chain 'E' and resid 443 through 458 Processing helix chain 'E' and resid 461 through 469 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 removed outlier: 8.901A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 92 removed outlier: 8.191A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE B 163 " --> pdb=" O GLN B 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 91 through 92 removed outlier: 8.191A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE B 163 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA7, first strand: chain 'H' and resid 91 through 92 removed outlier: 8.192A pdb=" N ILE H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU H 65 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE H 163 " --> pdb=" O GLN H 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 91 through 92 removed outlier: 8.192A pdb=" N ILE H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU H 65 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE H 163 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET H 164 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N TYR H 200 " --> pdb=" O MET H 164 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR H 166 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR H 199 " --> pdb=" O PHE H 266 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE H 265 " --> pdb=" O SER H 371 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER H 371 " --> pdb=" O PHE H 265 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 51 through 54 Processing sheet with id=AB1, first strand: chain 'K' and resid 93 through 94 removed outlier: 8.901A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'K' and resid 269 through 273 Processing sheet with id=AB4, first strand: chain 'C' and resid 240 through 244 removed outlier: 6.413A pdb=" N VAL C 240 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE C 264 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN C 242 " --> pdb=" O ILE C 264 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 240 through 244 removed outlier: 6.412A pdb=" N VAL E 240 " --> pdb=" O LEU E 262 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE E 264 " --> pdb=" O VAL E 240 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN E 242 " --> pdb=" O ILE E 264 " (cutoff:3.500A) 988 hydrogen bonds defined for protein. 2850 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: 3.15 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5078 1.33 - 1.46: 4571 1.46 - 1.58: 9717 1.58 - 1.70: 16 1.70 - 1.83: 194 Bond restraints: 19576 Sorted by residual: bond pdb=" CA THR E 284 " pdb=" C THR E 284 " ideal model delta sigma weight residual 1.524 1.543 -0.019 7.00e-03 2.04e+04 7.11e+00 bond pdb=" CA THR C 284 " pdb=" C THR C 284 " ideal model delta sigma weight residual 1.524 1.543 -0.019 7.00e-03 2.04e+04 7.03e+00 bond pdb=" CA LEU E 274 " pdb=" C LEU E 274 " ideal model delta sigma weight residual 1.523 1.556 -0.032 1.30e-02 5.92e+03 6.20e+00 bond pdb=" C GLU C 275 " pdb=" O GLU C 275 " ideal model delta sigma weight residual 1.236 1.208 0.029 1.18e-02 7.18e+03 6.03e+00 bond pdb=" CA LEU C 274 " pdb=" C LEU C 274 " ideal model delta sigma weight residual 1.523 1.555 -0.032 1.30e-02 5.92e+03 6.00e+00 ... (remaining 19571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 25671 2.13 - 4.26: 821 4.26 - 6.39: 61 6.39 - 8.53: 5 8.53 - 10.66: 3 Bond angle restraints: 26561 Sorted by residual: angle pdb=" N LEU C 325 " pdb=" CA LEU C 325 " pdb=" C LEU C 325 " ideal model delta sigma weight residual 111.02 117.79 -6.77 1.22e+00 6.72e-01 3.08e+01 angle pdb=" N LEU E 325 " pdb=" CA LEU E 325 " pdb=" C LEU E 325 " ideal model delta sigma weight residual 111.02 117.76 -6.74 1.22e+00 6.72e-01 3.06e+01 angle pdb=" C PRO H 357 " pdb=" N PRO H 358 " pdb=" CA PRO H 358 " ideal model delta sigma weight residual 119.84 126.53 -6.69 1.25e+00 6.40e-01 2.87e+01 angle pdb=" CA GLN C 271 " pdb=" CB GLN C 271 " pdb=" CG GLN C 271 " ideal model delta sigma weight residual 114.10 124.76 -10.66 2.00e+00 2.50e-01 2.84e+01 angle pdb=" CA GLN E 271 " pdb=" CB GLN E 271 " pdb=" CG GLN E 271 " ideal model delta sigma weight residual 114.10 124.76 -10.66 2.00e+00 2.50e-01 2.84e+01 ... (remaining 26556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.70: 11404 32.70 - 65.40: 221 65.40 - 98.10: 32 98.10 - 130.80: 2 130.80 - 163.50: 3 Dihedral angle restraints: 11662 sinusoidal: 4723 harmonic: 6939 Sorted by residual: dihedral pdb=" CA VAL K 440 " pdb=" C VAL K 440 " pdb=" N ARG C 259 " pdb=" CA ARG C 259 " ideal model delta harmonic sigma weight residual 180.00 19.59 160.41 0 5.00e+00 4.00e-02 1.03e+03 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -127.23 -163.50 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" C5' GTP K 501 " pdb=" O5' GTP K 501 " pdb=" PA GTP K 501 " pdb=" O3A GTP K 501 " ideal model delta sinusoidal sigma weight residual 69.27 -127.24 -163.49 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 11659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2483 0.071 - 0.142: 379 0.142 - 0.213: 14 0.213 - 0.284: 2 0.284 - 0.355: 2 Chirality restraints: 2880 Sorted by residual: chirality pdb=" CA ARG H 359 " pdb=" N ARG H 359 " pdb=" C ARG H 359 " pdb=" CB ARG H 359 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA ARG B 359 " pdb=" N ARG B 359 " pdb=" C ARG B 359 " pdb=" CB ARG B 359 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA VAL E 437 " pdb=" N VAL E 437 " pdb=" C VAL E 437 " pdb=" CB VAL E 437 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 2877 not shown) Planarity restraints: 3462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL K 440 " -0.025 2.00e-02 2.50e+03 5.65e-02 3.20e+01 pdb=" C VAL K 440 " 0.073 2.00e-02 2.50e+03 pdb=" O VAL K 440 " -0.077 2.00e-02 2.50e+03 pdb=" N ARG C 259 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 333 " 0.025 2.00e-02 2.50e+03 1.80e-02 8.08e+00 pdb=" CG TRP C 333 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP C 333 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP C 333 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP C 333 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP C 333 " 0.025 2.00e-02 2.50e+03 pdb=" CE3 TRP C 333 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 333 " 0.030 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 333 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 333 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 333 " 0.025 2.00e-02 2.50e+03 1.80e-02 8.07e+00 pdb=" CG TRP E 333 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP E 333 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP E 333 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP E 333 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP E 333 " 0.025 2.00e-02 2.50e+03 pdb=" CE3 TRP E 333 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 333 " 0.030 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 333 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP E 333 " -0.014 2.00e-02 2.50e+03 ... (remaining 3459 not shown) Histogram of nonbonded interaction distances: 0.62 - 1.48: 13 1.48 - 2.33: 126 2.33 - 3.19: 18423 3.19 - 4.04: 50061 4.04 - 4.90: 92420 Warning: very small nonbonded interaction distances. Nonbonded interactions: 161043 Sorted by model distance: nonbonded pdb=" CB SER K 439 " pdb=" CB ARG C 259 " model vdw 0.624 3.840 nonbonded pdb=" NH2 ARG B 391 " pdb=" NH1 ARG E 259 " model vdw 0.846 3.200 nonbonded pdb=" OE1 GLU K 434 " pdb=" NE2 GLN C 242 " model vdw 0.934 3.120 nonbonded pdb=" OG SER K 439 " pdb=" CD ARG C 259 " model vdw 0.985 3.440 nonbonded pdb=" O VAL A 437 " pdb=" NH2 ARG E 259 " model vdw 1.051 3.120 ... (remaining 161038 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 502)) selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.790 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4804 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 : 0.012 1.393 19582 Z= 0.794 Angle : 1.087 98.552 26564 Z= 0.684 Chirality : 0.049 0.355 2880 Planarity : 0.004 0.032 3461 Dihedral : 13.978 163.503 7203 Min Nonbonded Distance : 0.624 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 3.95 % Allowed : 6.73 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.17), residues: 2372 helix: -0.06 (0.14), residues: 1190 sheet: -1.41 (0.32), residues: 268 loop : -1.36 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 144 TYR 0.024 0.003 TYR E 370 PHE 0.020 0.002 PHE E 326 TRP 0.030 0.003 TRP C 333 HIS 0.012 0.002 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00624 (19576) covalent geometry : angle 0.84824 (26561) hydrogen bonds : bond 0.15154 ( 976) hydrogen bonds : angle 6.94371 ( 2850) metal coordination : bond 0.15601 ( 4) Misc. bond : bond 0.01134 ( 1) link_TRANS : bond 1.39273 ( 1) link_TRANS : angle 63.95284 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 650 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.5506 (mt) cc_final: 0.5255 (mm) REVERT: A 182 VAL cc_start: 0.4924 (m) cc_final: 0.4695 (t) REVERT: B 118 ASP cc_start: 0.7243 (m-30) cc_final: 0.7008 (m-30) REVERT: H 64 ILE cc_start: 0.6622 (mt) cc_final: 0.6365 (mt) REVERT: H 118 ASP cc_start: 0.6792 (m-30) cc_final: 0.6505 (m-30) REVERT: H 167 PHE cc_start: 0.5167 (m-80) cc_final: 0.4528 (m-10) REVERT: H 398 TYR cc_start: 0.6959 (m-80) cc_final: 0.6684 (m-80) REVERT: K 33 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6719 (p0) REVERT: K 128 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6981 (pp30) REVERT: K 154 MET cc_start: 0.8287 (mmm) cc_final: 0.8072 (mmm) REVERT: K 245 ASP cc_start: 0.7206 (t0) cc_final: 0.6855 (p0) REVERT: K 285 GLN cc_start: 0.7495 (pt0) cc_final: 0.6320 (mm-40) REVERT: K 370 LYS cc_start: 0.8263 (tttp) cc_final: 0.7923 (tppt) REVERT: K 382 THR cc_start: 0.6736 (OUTLIER) cc_final: 0.6525 (p) outliers start: 81 outliers final: 19 residues processed: 713 average time/residue: 0.6042 time to fit residues: 485.2608 Evaluate side-chains 398 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 376 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain K residue 33 ASP Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 112 LYS Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain K residue 200 CYS Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 382 THR Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain K residue 440 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 0.1980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 50.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS B 245 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN H 8 GLN ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN K 186 ASN ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 329 ASN K 406 HIS C 265 ASN E 242 GLN E 265 ASN E 378 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5282 r_free = 0.5282 target = 0.228509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.164461 restraints weight = 29182.208| |-----------------------------------------------------------------------------| r_work (start): 0.4555 rms_B_bonded: 3.18 r_work (final): 0.4555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4553 r_free = 0.4553 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4555 r_free = 0.4555 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 19582 Z= 0.271 Angle : 0.860 17.139 26564 Z= 0.454 Chirality : 0.052 0.341 2880 Planarity : 0.007 0.118 3461 Dihedral : 10.586 179.791 2713 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.75 % Favored : 96.08 % Rotamer: Outliers : 6.00 % Allowed : 17.47 % Favored : 76.53 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.17), residues: 2372 helix: 0.53 (0.14), residues: 1210 sheet: -1.33 (0.30), residues: 310 loop : -1.06 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 390 TYR 0.029 0.002 TYR B 51 PHE 0.033 0.003 PHE K 149 TRP 0.033 0.003 TRP C 223 HIS 0.014 0.002 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00584 (19576) covalent geometry : angle 0.85290 (26561) hydrogen bonds : bond 0.05397 ( 976) hydrogen bonds : angle 5.26826 ( 2850) metal coordination : bond 0.00661 ( 4) Misc. bond : bond 0.00816 ( 1) link_TRANS : bond 0.06072 ( 1) link_TRANS : angle 10.51736 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 430 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.5894 (ptp-110) REVERT: A 101 ASN cc_start: 0.7417 (t0) cc_final: 0.7061 (t0) REVERT: A 120 ASP cc_start: 0.7579 (m-30) cc_final: 0.6980 (m-30) REVERT: A 141 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7843 (t80) REVERT: A 199 ASP cc_start: 0.7850 (m-30) cc_final: 0.7340 (m-30) REVERT: A 293 ASN cc_start: 0.7997 (t0) cc_final: 0.7542 (t0) REVERT: A 413 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.6915 (ttm) REVERT: A 417 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7333 (tm-30) REVERT: A 424 ASP cc_start: 0.8486 (m-30) cc_final: 0.8217 (m-30) REVERT: A 438 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7842 (p0) REVERT: B 90 PHE cc_start: 0.7479 (m-10) cc_final: 0.7124 (m-80) REVERT: B 122 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7172 (ttmt) REVERT: B 162 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7885 (tpp-160) REVERT: B 164 MET cc_start: 0.7311 (mtp) cc_final: 0.7027 (mtp) REVERT: H 122 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7835 (ptpp) REVERT: H 128 ASP cc_start: 0.7895 (p0) cc_final: 0.7660 (p0) REVERT: H 159 TYR cc_start: 0.8464 (m-80) cc_final: 0.8245 (m-80) REVERT: H 198 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: H 249 ASP cc_start: 0.6852 (OUTLIER) cc_final: 0.6307 (p0) REVERT: H 285 THR cc_start: 0.7599 (p) cc_final: 0.7186 (t) REVERT: H 287 PRO cc_start: 0.8258 (Cg_exo) cc_final: 0.7820 (Cg_endo) REVERT: H 300 MET cc_start: 0.6134 (mtt) cc_final: 0.5930 (mtt) REVERT: H 323 MET cc_start: 0.8228 (tpt) cc_final: 0.7761 (tpp) REVERT: H 363 MET cc_start: 0.6198 (pp-130) cc_final: 0.5960 (ppp) REVERT: K 2 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6514 (tpt170) REVERT: K 154 MET cc_start: 0.8389 (mmm) cc_final: 0.7964 (mmp) REVERT: K 221 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7331 (mtt-85) REVERT: K 245 ASP cc_start: 0.7827 (t0) cc_final: 0.7582 (p0) REVERT: K 285 GLN cc_start: 0.8024 (pt0) cc_final: 0.6938 (mm-40) REVERT: K 304 LYS cc_start: 0.8863 (tppt) cc_final: 0.8648 (tppt) REVERT: K 309 HIS cc_start: 0.7223 (m-70) cc_final: 0.6774 (m-70) REVERT: K 370 LYS cc_start: 0.8402 (tttp) cc_final: 0.8185 (tptp) REVERT: K 382 THR cc_start: 0.6880 (OUTLIER) cc_final: 0.6488 (p) REVERT: K 384 ILE cc_start: 0.7038 (tp) cc_final: 0.6715 (tt) REVERT: K 437 VAL cc_start: 0.2374 (OUTLIER) cc_final: 0.1715 (m) REVERT: C 259 ARG cc_start: -0.0016 (ttm170) cc_final: -0.0554 (mtp-110) REVERT: E 329 GLN cc_start: 0.3014 (OUTLIER) cc_final: 0.2364 (pp30) REVERT: E 444 LEU cc_start: 0.7119 (mm) cc_final: 0.6807 (tp) outliers start: 123 outliers final: 36 residues processed: 511 average time/residue: 0.6018 time to fit residues: 347.4236 Evaluate side-chains 382 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 332 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 198 GLU Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 324 LYS Chi-restraints excluded: chain H residue 385 PHE Chi-restraints excluded: chain H residue 403 MET Chi-restraints excluded: chain K residue 2 ARG Chi-restraints excluded: chain K residue 112 LYS Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 221 ARG Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 305 CYS Chi-restraints excluded: chain K residue 318 LEU Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain K residue 382 THR Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 329 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 192 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 179 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 205 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 35 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS A 256 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN ** K 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 256 GLN ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 434 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5229 r_free = 0.5229 target = 0.230089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.161712 restraints weight = 29708.665| |-----------------------------------------------------------------------------| r_work (start): 0.4548 rms_B_bonded: 3.62 r_work: 0.4266 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4231 r_free = 0.4231 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4231 r_free = 0.4231 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.6343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 19582 Z= 0.203 Angle : 0.730 15.132 26564 Z= 0.377 Chirality : 0.046 0.208 2880 Planarity : 0.006 0.110 3461 Dihedral : 9.845 175.631 2692 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 5.03 % Allowed : 20.84 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.17), residues: 2372 helix: 0.86 (0.15), residues: 1206 sheet: -1.03 (0.29), residues: 320 loop : -0.96 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 123 TYR 0.017 0.002 TYR H 208 PHE 0.025 0.002 PHE H 20 TRP 0.017 0.002 TRP K 388 HIS 0.009 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00412 (19576) covalent geometry : angle 0.72289 (26561) hydrogen bonds : bond 0.04737 ( 976) hydrogen bonds : angle 4.94323 ( 2850) metal coordination : bond 0.00038 ( 4) Misc. bond : bond 0.00545 ( 1) link_TRANS : bond 0.07741 ( 1) link_TRANS : angle 9.48297 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 395 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.6457 (pmm150) REVERT: A 101 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7464 (t0) REVERT: A 141 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7866 (t80) REVERT: A 379 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.8073 (t) REVERT: A 417 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7318 (tm-30) REVERT: A 424 ASP cc_start: 0.8509 (m-30) cc_final: 0.8208 (m-30) REVERT: B 90 PHE cc_start: 0.7807 (m-10) cc_final: 0.7454 (m-80) REVERT: B 122 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7432 (ttmt) REVERT: B 162 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7834 (tpp-160) REVERT: B 164 MET cc_start: 0.7867 (mtp) cc_final: 0.7563 (mtp) REVERT: B 233 MET cc_start: 0.7659 (mmm) cc_final: 0.7442 (mtt) REVERT: B 363 MET cc_start: 0.7540 (pp-130) cc_final: 0.7139 (pp-130) REVERT: B 390 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8205 (ttm170) REVERT: H 50 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.7574 (m-10) REVERT: H 159 TYR cc_start: 0.8546 (m-80) cc_final: 0.8267 (m-80) REVERT: H 163 ILE cc_start: 0.7878 (tp) cc_final: 0.7600 (tp) REVERT: H 189 ILE cc_start: 0.8106 (mt) cc_final: 0.7813 (mt) REVERT: H 198 GLU cc_start: 0.7716 (mp0) cc_final: 0.7373 (mp0) REVERT: H 233 MET cc_start: 0.5550 (mmp) cc_final: 0.5313 (mmm) REVERT: H 288 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6535 (tm-30) REVERT: H 291 GLN cc_start: 0.7591 (tp40) cc_final: 0.7053 (pt0) REVERT: H 293 MET cc_start: 0.6715 (OUTLIER) cc_final: 0.6367 (mtt) REVERT: H 323 MET cc_start: 0.8248 (tpt) cc_final: 0.8045 (tpp) REVERT: K 2 ARG cc_start: 0.6663 (pmm150) cc_final: 0.6428 (tpt170) REVERT: K 154 MET cc_start: 0.8776 (mmm) cc_final: 0.8568 (mmm) REVERT: K 245 ASP cc_start: 0.8077 (t0) cc_final: 0.7860 (p0) REVERT: K 285 GLN cc_start: 0.7858 (pt0) cc_final: 0.6992 (mm-40) REVERT: K 301 GLN cc_start: 0.6459 (OUTLIER) cc_final: 0.6149 (pm20) REVERT: K 304 LYS cc_start: 0.8827 (tppt) cc_final: 0.8432 (tppt) REVERT: K 309 HIS cc_start: 0.7510 (m-70) cc_final: 0.6954 (m-70) REVERT: K 352 LYS cc_start: 0.4422 (tppt) cc_final: 0.4212 (tppt) REVERT: K 370 LYS cc_start: 0.8349 (tttp) cc_final: 0.7838 (tppt) REVERT: K 372 GLN cc_start: 0.7561 (pt0) cc_final: 0.7244 (pm20) REVERT: K 382 THR cc_start: 0.7421 (OUTLIER) cc_final: 0.7063 (p) REVERT: K 424 ASP cc_start: 0.8216 (t70) cc_final: 0.7583 (m-30) REVERT: K 430 LYS cc_start: 0.8293 (tmmt) cc_final: 0.7716 (mmpt) REVERT: E 148 MET cc_start: 0.4073 (mmm) cc_final: 0.3857 (mmm) REVERT: E 329 GLN cc_start: 0.2792 (OUTLIER) cc_final: 0.2282 (pp30) REVERT: E 422 ASP cc_start: 0.3157 (m-30) cc_final: 0.2434 (t70) outliers start: 103 outliers final: 40 residues processed: 469 average time/residue: 0.6227 time to fit residues: 329.2010 Evaluate side-chains 377 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 324 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 293 MET Chi-restraints excluded: chain H residue 304 ASP Chi-restraints excluded: chain H residue 318 ARG Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain K residue 241 SER Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 301 GLN Chi-restraints excluded: chain K residue 305 CYS Chi-restraints excluded: chain K residue 382 THR Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 329 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 43 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 211 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 247 ASN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 ASN ** K 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 ASN ** K 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN K 206 ASN ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5173 r_free = 0.5173 target = 0.220542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.142448 restraints weight = 28923.853| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 3.53 r_work: 0.4159 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.7177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 19582 Z= 0.185 Angle : 0.709 14.854 26564 Z= 0.366 Chirality : 0.045 0.235 2880 Planarity : 0.005 0.094 3461 Dihedral : 9.566 159.756 2683 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.08 % Rotamer: Outliers : 6.00 % Allowed : 22.01 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.17), residues: 2372 helix: 0.85 (0.15), residues: 1208 sheet: -0.76 (0.30), residues: 300 loop : -0.93 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 123 TYR 0.013 0.001 TYR B 159 PHE 0.030 0.002 PHE A 138 TRP 0.017 0.002 TRP K 388 HIS 0.010 0.001 HIS K 197 Details of bonding type rmsd covalent geometry : bond 0.00414 (19576) covalent geometry : angle 0.70193 (26561) hydrogen bonds : bond 0.04581 ( 976) hydrogen bonds : angle 4.85695 ( 2850) metal coordination : bond 0.00158 ( 4) Misc. bond : bond 0.00538 ( 1) link_TRANS : bond 0.06978 ( 1) link_TRANS : angle 9.48460 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 347 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5782 (OUTLIER) cc_final: 0.5336 (ppp) REVERT: A 101 ASN cc_start: 0.7886 (OUTLIER) cc_final: 0.7453 (t0) REVERT: A 141 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7613 (t80) REVERT: A 172 TYR cc_start: 0.5847 (t80) cc_final: 0.5602 (t80) REVERT: A 176 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8341 (mp10) REVERT: A 203 MET cc_start: 0.6351 (mmm) cc_final: 0.5979 (mmt) REVERT: A 413 MET cc_start: 0.7993 (ttm) cc_final: 0.7199 (ttt) REVERT: A 424 ASP cc_start: 0.8603 (m-30) cc_final: 0.8115 (m-30) REVERT: B 58 LYS cc_start: 0.2086 (pttt) cc_final: 0.1557 (tmmt) REVERT: B 156 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.8037 (ttm-80) REVERT: B 162 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7821 (tpp-160) REVERT: B 164 MET cc_start: 0.7814 (mtp) cc_final: 0.7492 (ttm) REVERT: B 284 LEU cc_start: 0.8015 (tp) cc_final: 0.7803 (pt) REVERT: B 363 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7087 (pp-130) REVERT: B 390 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8093 (ttm170) REVERT: H 50 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.7780 (m-10) REVERT: H 128 ASP cc_start: 0.8462 (p0) cc_final: 0.8256 (p0) REVERT: H 198 GLU cc_start: 0.7665 (mp0) cc_final: 0.7413 (mp0) REVERT: H 293 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6473 (mtt) REVERT: H 320 ARG cc_start: 0.6324 (tpp-160) cc_final: 0.6079 (tpp-160) REVERT: H 321 MET cc_start: 0.7022 (ptp) cc_final: 0.6075 (ptp) REVERT: H 330 MET cc_start: 0.7537 (tpp) cc_final: 0.7229 (tmm) REVERT: H 336 LYS cc_start: 0.8627 (pptt) cc_final: 0.8046 (mttp) REVERT: H 388 MET cc_start: 0.6533 (tpp) cc_final: 0.6295 (mmt) REVERT: K 304 LYS cc_start: 0.8635 (tppt) cc_final: 0.8299 (tppt) REVERT: K 309 HIS cc_start: 0.7610 (m-70) cc_final: 0.7021 (m-70) REVERT: K 370 LYS cc_start: 0.8400 (tttp) cc_final: 0.7846 (tppt) REVERT: K 382 THR cc_start: 0.7671 (OUTLIER) cc_final: 0.7292 (p) REVERT: K 417 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8555 (tm-30) REVERT: K 424 ASP cc_start: 0.8316 (t70) cc_final: 0.7821 (m-30) REVERT: K 425 MET cc_start: 0.8874 (mmm) cc_final: 0.8345 (tpp) REVERT: K 430 LYS cc_start: 0.8583 (tmmt) cc_final: 0.7813 (mmpt) REVERT: C 348 MET cc_start: 0.4888 (mpp) cc_final: 0.4421 (pmm) REVERT: E 329 GLN cc_start: 0.2890 (OUTLIER) cc_final: 0.2245 (pp30) outliers start: 123 outliers final: 48 residues processed: 431 average time/residue: 0.6172 time to fit residues: 299.9773 Evaluate side-chains 359 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 299 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain H residue 293 MET Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 318 ARG Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 219 ILE Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain K residue 382 THR Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 329 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 81 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 220 optimal weight: 7.9990 chunk 170 optimal weight: 50.0000 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 0.0370 chunk 69 optimal weight: 0.5980 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 50 ASN B 6 HIS B 105 HIS ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 ASN ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN ** K 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 197 HIS ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN E 242 GLN E 329 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5143 r_free = 0.5143 target = 0.214777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.140662 restraints weight = 27420.357| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 4.62 r_work: 0.4076 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.7682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19582 Z= 0.160 Angle : 0.701 14.696 26564 Z= 0.359 Chirality : 0.045 0.210 2880 Planarity : 0.005 0.096 3461 Dihedral : 9.390 152.159 2683 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 5.17 % Allowed : 22.21 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.17), residues: 2372 helix: 0.91 (0.15), residues: 1188 sheet: -0.90 (0.30), residues: 296 loop : -0.75 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 123 TYR 0.019 0.001 TYR H 340 PHE 0.045 0.002 PHE C 409 TRP 0.013 0.001 TRP K 388 HIS 0.010 0.001 HIS K 8 Details of bonding type rmsd covalent geometry : bond 0.00355 (19576) covalent geometry : angle 0.69398 (26561) hydrogen bonds : bond 0.04297 ( 976) hydrogen bonds : angle 4.78615 ( 2850) metal coordination : bond 0.00062 ( 4) Misc. bond : bond 0.00731 ( 1) link_TRANS : bond 0.06594 ( 1) link_TRANS : angle 9.21406 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 346 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5773 (pp-130) cc_final: 0.5332 (ppp) REVERT: A 35 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6631 (mp10) REVERT: A 101 ASN cc_start: 0.7812 (OUTLIER) cc_final: 0.7475 (t0) REVERT: A 141 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7506 (t80) REVERT: A 176 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8710 (mp10) REVERT: A 192 HIS cc_start: 0.7971 (t-90) cc_final: 0.7757 (t-170) REVERT: A 203 MET cc_start: 0.6791 (mmm) cc_final: 0.6503 (mmt) REVERT: A 417 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: B 58 LYS cc_start: 0.2393 (pttt) cc_final: 0.1884 (tmmt) REVERT: B 89 ASN cc_start: 0.7129 (m-40) cc_final: 0.6803 (m110) REVERT: B 156 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7926 (ttm-80) REVERT: B 162 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7877 (tpp-160) REVERT: B 284 LEU cc_start: 0.8095 (tp) cc_final: 0.7876 (pt) REVERT: B 299 MET cc_start: 0.7371 (mtt) cc_final: 0.6992 (mtt) REVERT: B 363 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7079 (pp-130) REVERT: B 390 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8059 (ttm170) REVERT: H 50 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.7920 (m-10) REVERT: H 85 PHE cc_start: 0.5932 (OUTLIER) cc_final: 0.5487 (t80) REVERT: H 128 ASP cc_start: 0.8574 (p0) cc_final: 0.8276 (p0) REVERT: H 198 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: H 240 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7224 (pt) REVERT: H 321 MET cc_start: 0.7011 (ptp) cc_final: 0.5979 (ptp) REVERT: H 336 LYS cc_start: 0.8645 (pptt) cc_final: 0.8027 (mttp) REVERT: H 388 MET cc_start: 0.6472 (tpp) cc_final: 0.6237 (mmt) REVERT: K 1 MET cc_start: 0.7922 (tmt) cc_final: 0.7687 (tmm) REVERT: K 215 ARG cc_start: 0.6630 (ttm110) cc_final: 0.6135 (mtm-85) REVERT: K 285 GLN cc_start: 0.7929 (pm20) cc_final: 0.6952 (mm-40) REVERT: K 304 LYS cc_start: 0.8665 (tppt) cc_final: 0.8277 (tppt) REVERT: K 370 LYS cc_start: 0.8409 (tttp) cc_final: 0.7870 (tppt) REVERT: K 382 THR cc_start: 0.7603 (OUTLIER) cc_final: 0.6918 (p) REVERT: K 388 TRP cc_start: 0.7891 (m100) cc_final: 0.7614 (m100) REVERT: K 424 ASP cc_start: 0.8422 (t70) cc_final: 0.8003 (m-30) REVERT: K 425 MET cc_start: 0.8965 (mmm) cc_final: 0.8353 (tpp) REVERT: K 430 LYS cc_start: 0.8651 (tmmt) cc_final: 0.7990 (mmpt) REVERT: K 432 TYR cc_start: 0.7293 (OUTLIER) cc_final: 0.5416 (t80) REVERT: C 348 MET cc_start: 0.5736 (mpp) cc_final: 0.5265 (pmm) REVERT: C 461 ASP cc_start: 0.5296 (p0) cc_final: 0.5088 (p0) REVERT: E 148 MET cc_start: 0.3311 (mmm) cc_final: 0.2728 (mmm) REVERT: E 329 GLN cc_start: 0.2988 (OUTLIER) cc_final: 0.2331 (pp30) REVERT: E 342 ILE cc_start: 0.1556 (mt) cc_final: 0.1269 (mm) outliers start: 106 outliers final: 54 residues processed: 425 average time/residue: 0.5748 time to fit residues: 277.3922 Evaluate side-chains 382 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 312 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 85 PHE Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 198 GLU Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 257 MET Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 318 ARG Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain K residue 382 THR Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 440 VAL Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 329 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 207 optimal weight: 40.0000 chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 0.0270 chunk 37 optimal weight: 3.9990 chunk 203 optimal weight: 50.0000 chunk 109 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 192 optimal weight: 30.0000 chunk 168 optimal weight: 2.9990 overall best weight: 2.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 HIS H 126 ASN ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 HIS K 101 ASN ** K 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN E 242 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5128 r_free = 0.5128 target = 0.203589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.127032 restraints weight = 26550.802| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 3.88 r_work: 0.3927 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.8662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 19582 Z= 0.269 Angle : 0.796 14.556 26564 Z= 0.412 Chirality : 0.049 0.302 2880 Planarity : 0.006 0.092 3461 Dihedral : 9.515 144.517 2683 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.01 % Favored : 95.91 % Rotamer: Outliers : 6.00 % Allowed : 24.01 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.17), residues: 2372 helix: 0.75 (0.15), residues: 1188 sheet: -0.99 (0.31), residues: 288 loop : -0.88 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 308 TYR 0.028 0.002 TYR H 36 PHE 0.036 0.003 PHE H 167 TRP 0.016 0.002 TRP E 223 HIS 0.028 0.002 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00614 (19576) covalent geometry : angle 0.79062 (26561) hydrogen bonds : bond 0.05199 ( 976) hydrogen bonds : angle 5.07292 ( 2850) metal coordination : bond 0.00095 ( 4) Misc. bond : bond 0.00695 ( 1) link_TRANS : bond 0.06313 ( 1) link_TRANS : angle 9.07012 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 324 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6003 (pp-130) cc_final: 0.5669 (ppp) REVERT: A 75 ILE cc_start: 0.8671 (mm) cc_final: 0.8375 (mm) REVERT: A 101 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7754 (t0) REVERT: A 123 ARG cc_start: 0.8444 (ttp80) cc_final: 0.7877 (tmm160) REVERT: A 133 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7685 (mt0) REVERT: A 141 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7647 (t80) REVERT: A 176 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8766 (mp10) REVERT: A 417 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7481 (tt0) REVERT: A 424 ASP cc_start: 0.8384 (m-30) cc_final: 0.8114 (m-30) REVERT: B 58 LYS cc_start: 0.2788 (pttt) cc_final: 0.2027 (tmmt) REVERT: B 89 ASN cc_start: 0.7103 (m-40) cc_final: 0.6713 (m110) REVERT: B 156 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7849 (ttm-80) REVERT: B 279 GLN cc_start: 0.8100 (pm20) cc_final: 0.7879 (pm20) REVERT: B 280 GLN cc_start: 0.8062 (pm20) cc_final: 0.7750 (pm20) REVERT: B 299 MET cc_start: 0.7330 (mtt) cc_final: 0.7058 (mtm) REVERT: B 363 MET cc_start: 0.7563 (pp-130) cc_final: 0.7034 (pp-130) REVERT: B 390 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8236 (ttm170) REVERT: H 50 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.8190 (m-10) REVERT: H 85 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.5832 (t80) REVERT: H 128 ASP cc_start: 0.8554 (p0) cc_final: 0.8090 (p0) REVERT: H 174 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8734 (mppt) REVERT: H 200 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.7469 (m-80) REVERT: H 282 ARG cc_start: 0.7184 (tpp-160) cc_final: 0.6904 (tpp-160) REVERT: H 318 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.5709 (mtm180) REVERT: H 336 LYS cc_start: 0.8791 (pptt) cc_final: 0.8191 (mttp) REVERT: H 375 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8477 (pp30) REVERT: H 388 MET cc_start: 0.6983 (tpp) cc_final: 0.6575 (mmt) REVERT: K 1 MET cc_start: 0.7880 (tmt) cc_final: 0.7589 (tmm) REVERT: K 112 LYS cc_start: 0.8704 (pttt) cc_final: 0.8292 (pttt) REVERT: K 215 ARG cc_start: 0.6903 (ttm110) cc_final: 0.6494 (mtm-85) REVERT: K 252 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8823 (mt) REVERT: K 285 GLN cc_start: 0.8091 (pm20) cc_final: 0.7331 (mm-40) REVERT: K 304 LYS cc_start: 0.8630 (tppt) cc_final: 0.8352 (tppt) REVERT: K 345 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8080 (p0) REVERT: K 370 LYS cc_start: 0.8242 (tttp) cc_final: 0.7775 (tppt) REVERT: K 377 MET cc_start: 0.7605 (ttp) cc_final: 0.7019 (ttp) REVERT: K 382 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7833 (p) REVERT: K 424 ASP cc_start: 0.8531 (t70) cc_final: 0.8146 (m-30) REVERT: K 425 MET cc_start: 0.8878 (mmm) cc_final: 0.8323 (tpp) REVERT: K 430 LYS cc_start: 0.8663 (tmmt) cc_final: 0.8038 (mmtt) REVERT: K 432 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.5315 (t80) REVERT: C 348 MET cc_start: 0.5943 (mpp) cc_final: 0.5557 (pmm) REVERT: C 369 GLU cc_start: 0.3688 (tp30) cc_final: 0.3411 (tm-30) REVERT: E 148 MET cc_start: 0.3332 (mmm) cc_final: 0.2670 (mmm) outliers start: 123 outliers final: 52 residues processed: 422 average time/residue: 0.6043 time to fit residues: 288.3073 Evaluate side-chains 366 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 298 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 85 PHE Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 200 TYR Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 318 ARG Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain K residue 219 ILE Chi-restraints excluded: chain K residue 239 THR Chi-restraints excluded: chain K residue 252 LEU Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain K residue 382 THR Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 440 VAL Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 240 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 68 optimal weight: 0.9990 chunk 7 optimal weight: 0.0770 chunk 117 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 209 optimal weight: 50.0000 chunk 159 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 144 optimal weight: 0.3980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 50 ASN A 133 GLN A 256 GLN A 300 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN B 426 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 247 ASN ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN ** K 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5158 r_free = 0.5158 target = 0.206805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.136599 restraints weight = 26482.391| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 4.48 r_work: 0.3996 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.8850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19582 Z= 0.159 Angle : 0.718 12.964 26564 Z= 0.368 Chirality : 0.045 0.246 2880 Planarity : 0.005 0.090 3461 Dihedral : 9.146 143.215 2683 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.16 % Favored : 96.75 % Rotamer: Outliers : 4.39 % Allowed : 26.21 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.17), residues: 2372 helix: 0.82 (0.15), residues: 1202 sheet: -1.01 (0.30), residues: 298 loop : -0.70 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 121 TYR 0.025 0.001 TYR B 159 PHE 0.025 0.002 PHE A 49 TRP 0.017 0.001 TRP K 388 HIS 0.010 0.001 HIS K 197 Details of bonding type rmsd covalent geometry : bond 0.00349 (19576) covalent geometry : angle 0.71309 (26561) hydrogen bonds : bond 0.04359 ( 976) hydrogen bonds : angle 4.89327 ( 2850) metal coordination : bond 0.00081 ( 4) Misc. bond : bond 0.00741 ( 1) link_TRANS : bond 0.06192 ( 1) link_TRANS : angle 8.17488 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 336 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6200 (OUTLIER) cc_final: 0.5800 (ppp) REVERT: A 35 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6967 (mp10) REVERT: A 75 ILE cc_start: 0.8605 (mm) cc_final: 0.8365 (mm) REVERT: A 101 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7500 (t0) REVERT: A 123 ARG cc_start: 0.8434 (ttp80) cc_final: 0.7811 (tmm160) REVERT: A 176 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8795 (mp10) REVERT: A 192 HIS cc_start: 0.7887 (t-90) cc_final: 0.7667 (t70) REVERT: B 58 LYS cc_start: 0.2392 (pttt) cc_final: 0.1925 (ttpt) REVERT: B 89 ASN cc_start: 0.7152 (m-40) cc_final: 0.6859 (m110) REVERT: B 158 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7844 (mm-30) REVERT: B 279 GLN cc_start: 0.7986 (pm20) cc_final: 0.7691 (pm20) REVERT: B 299 MET cc_start: 0.7537 (mtt) cc_final: 0.7193 (mtt) REVERT: B 363 MET cc_start: 0.7529 (pp-130) cc_final: 0.6723 (pp-130) REVERT: B 390 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8142 (ttm170) REVERT: B 407 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: H 50 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.8178 (m-10) REVERT: H 85 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.6032 (t80) REVERT: H 118 ASP cc_start: 0.7256 (m-30) cc_final: 0.7031 (m-30) REVERT: H 128 ASP cc_start: 0.8621 (p0) cc_final: 0.8104 (p0) REVERT: H 191 GLN cc_start: 0.8154 (mm110) cc_final: 0.7799 (mm-40) REVERT: H 318 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.5732 (mtm180) REVERT: H 375 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8526 (pp30) REVERT: H 388 MET cc_start: 0.6916 (tpp) cc_final: 0.6704 (mmt) REVERT: K 1 MET cc_start: 0.7728 (tmt) cc_final: 0.7479 (tmm) REVERT: K 112 LYS cc_start: 0.8459 (pttt) cc_final: 0.8222 (pttt) REVERT: K 113 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7817 (mp0) REVERT: K 211 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8053 (t70) REVERT: K 215 ARG cc_start: 0.6971 (ttm110) cc_final: 0.6726 (mtm-85) REVERT: K 285 GLN cc_start: 0.7959 (pm20) cc_final: 0.7278 (mm-40) REVERT: K 304 LYS cc_start: 0.8622 (tppt) cc_final: 0.8047 (tppt) REVERT: K 345 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8234 (p0) REVERT: K 370 LYS cc_start: 0.8089 (tttp) cc_final: 0.7733 (tppt) REVERT: K 424 ASP cc_start: 0.8541 (t70) cc_final: 0.8253 (m-30) REVERT: K 425 MET cc_start: 0.8988 (mmm) cc_final: 0.8401 (tpp) REVERT: K 430 LYS cc_start: 0.8741 (tmmt) cc_final: 0.8085 (mmtt) REVERT: K 432 TYR cc_start: 0.7648 (OUTLIER) cc_final: 0.5598 (t80) REVERT: C 151 GLU cc_start: 0.4714 (mm-30) cc_final: 0.3982 (mt-10) REVERT: C 253 MET cc_start: 0.4002 (mmm) cc_final: 0.2557 (mpp) REVERT: C 348 MET cc_start: 0.6034 (mpp) cc_final: 0.5638 (pmm) REVERT: C 369 GLU cc_start: 0.3919 (tp30) cc_final: 0.3590 (tm-30) REVERT: E 148 MET cc_start: 0.2808 (mmm) cc_final: 0.2166 (mmm) outliers start: 90 outliers final: 41 residues processed: 401 average time/residue: 0.5914 time to fit residues: 268.5400 Evaluate side-chains 359 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 305 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 83 HIS Chi-restraints excluded: chain H residue 85 PHE Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain H residue 318 ARG Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain K residue 219 ILE Chi-restraints excluded: chain K residue 239 THR Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 240 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 179 optimal weight: 50.0000 chunk 206 optimal weight: 0.8980 chunk 183 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 chunk 88 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 300 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN K 101 ASN ** K 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 HIS E 242 GLN ** E 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.204303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.134246 restraints weight = 26366.703| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 4.11 r_work: 0.3927 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.9185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19582 Z= 0.185 Angle : 0.749 12.275 26564 Z= 0.386 Chirality : 0.046 0.234 2880 Planarity : 0.005 0.091 3461 Dihedral : 9.088 144.993 2682 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.50 % Favored : 96.42 % Rotamer: Outliers : 4.29 % Allowed : 27.09 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.17), residues: 2372 helix: 0.85 (0.15), residues: 1190 sheet: -0.89 (0.30), residues: 304 loop : -0.68 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 427 TYR 0.029 0.002 TYR B 159 PHE 0.030 0.002 PHE H 167 TRP 0.013 0.002 TRP C 297 HIS 0.013 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00423 (19576) covalent geometry : angle 0.74473 (26561) hydrogen bonds : bond 0.04529 ( 976) hydrogen bonds : angle 4.94449 ( 2850) metal coordination : bond 0.00747 ( 4) Misc. bond : bond 0.00696 ( 1) link_TRANS : bond 0.06140 ( 1) link_TRANS : angle 7.83803 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 319 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6357 (OUTLIER) cc_final: 0.5928 (ppp) REVERT: A 75 ILE cc_start: 0.8671 (mm) cc_final: 0.8424 (mm) REVERT: A 101 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7605 (t0) REVERT: A 123 ARG cc_start: 0.8401 (ttp80) cc_final: 0.7994 (tmm160) REVERT: A 176 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8786 (mp10) REVERT: A 352 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8194 (tmtp) REVERT: A 424 ASP cc_start: 0.8290 (m-30) cc_final: 0.8062 (m-30) REVERT: B 58 LYS cc_start: 0.2644 (pttt) cc_final: 0.2001 (ttmt) REVERT: B 81 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.5310 (t80) REVERT: B 89 ASN cc_start: 0.7348 (m-40) cc_final: 0.6915 (m110) REVERT: B 279 GLN cc_start: 0.8153 (pm20) cc_final: 0.7758 (pm20) REVERT: B 299 MET cc_start: 0.7447 (mtt) cc_final: 0.7091 (mtt) REVERT: B 363 MET cc_start: 0.7590 (pp-130) cc_final: 0.7126 (pp-130) REVERT: B 390 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8225 (ttm170) REVERT: B 407 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: H 50 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.8206 (m-10) REVERT: H 128 ASP cc_start: 0.8583 (p0) cc_final: 0.8182 (p0) REVERT: H 174 LYS cc_start: 0.9286 (mmmm) cc_final: 0.8932 (mppt) REVERT: H 191 GLN cc_start: 0.8210 (mm110) cc_final: 0.7864 (mm-40) REVERT: H 281 TYR cc_start: 0.7047 (m-10) cc_final: 0.5946 (t80) REVERT: H 306 ARG cc_start: 0.8292 (mpt180) cc_final: 0.7998 (mpt180) REVERT: H 310 TYR cc_start: 0.7837 (m-80) cc_final: 0.7623 (m-80) REVERT: H 318 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.5779 (mtm180) REVERT: H 336 LYS cc_start: 0.8850 (pptt) cc_final: 0.8228 (mmtm) REVERT: H 375 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8449 (pp30) REVERT: H 388 MET cc_start: 0.6939 (tpp) cc_final: 0.6735 (mmt) REVERT: K 1 MET cc_start: 0.7839 (tmt) cc_final: 0.7542 (tmm) REVERT: K 113 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7799 (mp0) REVERT: K 215 ARG cc_start: 0.7073 (ttm110) cc_final: 0.6655 (mtm-85) REVERT: K 285 GLN cc_start: 0.8023 (pm20) cc_final: 0.7275 (mm-40) REVERT: K 304 LYS cc_start: 0.8622 (tppt) cc_final: 0.8320 (tppt) REVERT: K 345 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8252 (p0) REVERT: K 370 LYS cc_start: 0.8275 (tttp) cc_final: 0.7681 (tppt) REVERT: K 388 TRP cc_start: 0.7975 (m100) cc_final: 0.7575 (m100) REVERT: K 424 ASP cc_start: 0.8472 (t70) cc_final: 0.8182 (m-30) REVERT: K 425 MET cc_start: 0.8964 (mmm) cc_final: 0.8319 (tpp) REVERT: K 430 LYS cc_start: 0.8672 (tmmt) cc_final: 0.8074 (mmtt) REVERT: K 432 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.5670 (t80) REVERT: C 348 MET cc_start: 0.6005 (mpp) cc_final: 0.5709 (pmm) REVERT: E 148 MET cc_start: 0.3724 (mmm) cc_final: 0.3044 (mmm) outliers start: 88 outliers final: 44 residues processed: 378 average time/residue: 0.6249 time to fit residues: 266.1635 Evaluate side-chains 352 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 296 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 83 HIS Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 159 TYR Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 300 MET Chi-restraints excluded: chain H residue 318 ARG Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain K residue 219 ILE Chi-restraints excluded: chain K residue 239 THR Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 240 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 72 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 169 optimal weight: 0.9990 chunk 204 optimal weight: 50.0000 chunk 185 optimal weight: 20.0000 chunk 183 optimal weight: 30.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 329 ASN B 165 ASN ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5094 r_free = 0.5094 target = 0.209552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.127789 restraints weight = 26907.960| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 4.58 r_work: 0.3901 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.9457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 19582 Z= 0.173 Angle : 0.754 11.637 26564 Z= 0.386 Chirality : 0.047 0.328 2880 Planarity : 0.005 0.091 3461 Dihedral : 8.950 145.366 2682 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.71 % Favored : 96.21 % Rotamer: Outliers : 4.20 % Allowed : 27.53 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.18), residues: 2372 helix: 0.98 (0.15), residues: 1164 sheet: -1.00 (0.30), residues: 302 loop : -0.59 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 213 TYR 0.029 0.002 TYR B 159 PHE 0.027 0.002 PHE H 167 TRP 0.016 0.001 TRP K 388 HIS 0.012 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00397 (19576) covalent geometry : angle 0.74973 (26561) hydrogen bonds : bond 0.04460 ( 976) hydrogen bonds : angle 4.91505 ( 2850) metal coordination : bond 0.00070 ( 4) Misc. bond : bond 0.01126 ( 1) link_TRANS : bond 0.05964 ( 1) link_TRANS : angle 7.51933 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 312 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6425 (OUTLIER) cc_final: 0.5991 (ppp) REVERT: A 75 ILE cc_start: 0.8630 (mm) cc_final: 0.8291 (mt) REVERT: A 101 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7549 (t0) REVERT: A 123 ARG cc_start: 0.8385 (ttp80) cc_final: 0.8016 (tmm160) REVERT: A 176 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8670 (mp10) REVERT: A 211 ASP cc_start: 0.7774 (m-30) cc_final: 0.7464 (t70) REVERT: A 285 GLN cc_start: 0.8426 (pt0) cc_final: 0.7779 (mm110) REVERT: A 352 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8195 (tmtp) REVERT: B 58 LYS cc_start: 0.2673 (pttt) cc_final: 0.2082 (ttmt) REVERT: B 81 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6967 (t80) REVERT: B 89 ASN cc_start: 0.7283 (m-40) cc_final: 0.6945 (m110) REVERT: B 165 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.7787 (m110) REVERT: B 279 GLN cc_start: 0.8171 (pm20) cc_final: 0.7801 (pm20) REVERT: B 299 MET cc_start: 0.7534 (mtt) cc_final: 0.7171 (mtt) REVERT: B 363 MET cc_start: 0.7567 (pp-130) cc_final: 0.6984 (pp-130) REVERT: B 390 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8241 (ttm170) REVERT: B 403 MET cc_start: 0.8012 (ttp) cc_final: 0.7671 (ttm) REVERT: H 128 ASP cc_start: 0.8590 (p0) cc_final: 0.8121 (p0) REVERT: H 174 LYS cc_start: 0.9358 (mmmm) cc_final: 0.8969 (mppt) REVERT: H 191 GLN cc_start: 0.8150 (mm110) cc_final: 0.7864 (mm-40) REVERT: H 281 TYR cc_start: 0.7087 (m-10) cc_final: 0.5969 (t80) REVERT: H 284 LEU cc_start: 0.7207 (tp) cc_final: 0.6883 (tt) REVERT: H 299 MET cc_start: 0.6433 (pp-130) cc_final: 0.5277 (ptp) REVERT: H 310 TYR cc_start: 0.8054 (m-80) cc_final: 0.7822 (m-80) REVERT: H 320 ARG cc_start: 0.7409 (mpt180) cc_final: 0.7182 (tpp-160) REVERT: H 336 LYS cc_start: 0.8821 (pptt) cc_final: 0.8162 (mmtm) REVERT: H 375 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8364 (pp30) REVERT: H 379 LYS cc_start: 0.9087 (pptt) cc_final: 0.8828 (ptmm) REVERT: K 1 MET cc_start: 0.7792 (tmt) cc_final: 0.7530 (tmm) REVERT: K 113 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7798 (mp0) REVERT: K 285 GLN cc_start: 0.8144 (pm20) cc_final: 0.7401 (mm-40) REVERT: K 304 LYS cc_start: 0.8613 (tppt) cc_final: 0.8302 (tppt) REVERT: K 370 LYS cc_start: 0.8149 (tttp) cc_final: 0.7705 (tppt) REVERT: K 424 ASP cc_start: 0.8419 (t70) cc_final: 0.8140 (m-30) REVERT: K 425 MET cc_start: 0.8940 (mmm) cc_final: 0.8301 (tpp) REVERT: K 430 LYS cc_start: 0.8468 (tmmt) cc_final: 0.8014 (mmtt) REVERT: K 432 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.5651 (t80) REVERT: C 348 MET cc_start: 0.5759 (mpp) cc_final: 0.5537 (pmm) REVERT: E 148 MET cc_start: 0.4217 (mmm) cc_final: 0.3627 (mmm) REVERT: E 230 MET cc_start: 0.3320 (OUTLIER) cc_final: 0.2739 (tpt) outliers start: 86 outliers final: 54 residues processed: 374 average time/residue: 0.6083 time to fit residues: 257.4502 Evaluate side-chains 357 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 293 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 159 TYR Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 318 ARG Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain K residue 219 ILE Chi-restraints excluded: chain K residue 239 THR Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 74 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 210 optimal weight: 40.0000 chunk 29 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 83 optimal weight: 0.3980 chunk 155 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 329 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 372 GLN C 378 GLN ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.204112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.125870 restraints weight = 26381.026| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 3.62 r_work: 0.3898 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.9702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19582 Z= 0.193 Angle : 0.789 11.501 26564 Z= 0.405 Chirality : 0.048 0.307 2880 Planarity : 0.005 0.091 3461 Dihedral : 8.981 146.359 2682 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.16 % Rotamer: Outliers : 3.86 % Allowed : 28.31 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.17), residues: 2372 helix: 0.84 (0.15), residues: 1178 sheet: -1.03 (0.30), residues: 302 loop : -0.58 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 213 TYR 0.029 0.002 TYR B 159 PHE 0.033 0.002 PHE H 167 TRP 0.020 0.002 TRP A 388 HIS 0.010 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00446 (19576) covalent geometry : angle 0.78465 (26561) hydrogen bonds : bond 0.04676 ( 976) hydrogen bonds : angle 4.97606 ( 2850) metal coordination : bond 0.00134 ( 4) Misc. bond : bond 0.00957 ( 1) link_TRANS : bond 0.05877 ( 1) link_TRANS : angle 7.49960 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4744 Ramachandran restraints generated. 2372 Oldfield, 0 Emsley, 2372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 297 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6449 (pp-130) cc_final: 0.6007 (ppp) REVERT: A 75 ILE cc_start: 0.8700 (mm) cc_final: 0.8438 (mt) REVERT: A 94 THR cc_start: 0.7243 (OUTLIER) cc_final: 0.6985 (t) REVERT: A 101 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7634 (t0) REVERT: A 123 ARG cc_start: 0.8351 (ttp80) cc_final: 0.7993 (tmm160) REVERT: A 176 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8718 (mp10) REVERT: A 211 ASP cc_start: 0.7987 (m-30) cc_final: 0.7670 (t70) REVERT: A 285 GLN cc_start: 0.8415 (pt0) cc_final: 0.7763 (mm110) REVERT: A 352 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8302 (tmtp) REVERT: B 58 LYS cc_start: 0.2709 (pttt) cc_final: 0.2114 (ttmt) REVERT: B 81 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.7042 (t80) REVERT: B 157 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7547 (pp20) REVERT: B 279 GLN cc_start: 0.8146 (pm20) cc_final: 0.7720 (pm20) REVERT: B 330 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7399 (tmm) REVERT: B 363 MET cc_start: 0.7444 (pp-130) cc_final: 0.7052 (pp-130) REVERT: B 390 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8188 (ttm170) REVERT: H 86 ARG cc_start: 0.6783 (tpt170) cc_final: 0.6044 (tpp-160) REVERT: H 128 ASP cc_start: 0.8640 (p0) cc_final: 0.8228 (p0) REVERT: H 147 MET cc_start: 0.8144 (mmm) cc_final: 0.7940 (mmm) REVERT: H 174 LYS cc_start: 0.9333 (mmmm) cc_final: 0.8975 (mppt) REVERT: H 191 GLN cc_start: 0.8172 (mm110) cc_final: 0.7853 (mm-40) REVERT: H 281 TYR cc_start: 0.7232 (m-10) cc_final: 0.6171 (t80) REVERT: H 284 LEU cc_start: 0.7332 (tp) cc_final: 0.7038 (tt) REVERT: H 320 ARG cc_start: 0.7449 (mpt180) cc_final: 0.7144 (mpt180) REVERT: H 336 LYS cc_start: 0.8846 (pptt) cc_final: 0.8203 (mttp) REVERT: H 375 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8416 (pp30) REVERT: H 379 LYS cc_start: 0.9075 (pptt) cc_final: 0.8821 (ptmm) REVERT: K 1 MET cc_start: 0.7754 (tmt) cc_final: 0.7504 (tmm) REVERT: K 112 LYS cc_start: 0.8335 (pmtt) cc_final: 0.8101 (pmtt) REVERT: K 113 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7853 (mp0) REVERT: K 285 GLN cc_start: 0.8148 (pm20) cc_final: 0.7424 (mm-40) REVERT: K 304 LYS cc_start: 0.8608 (tppt) cc_final: 0.7921 (tppt) REVERT: K 345 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8348 (p0) REVERT: K 372 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7441 (pm20) REVERT: K 388 TRP cc_start: 0.7909 (m100) cc_final: 0.7568 (m100) REVERT: K 424 ASP cc_start: 0.8525 (t70) cc_final: 0.8272 (m-30) REVERT: K 425 MET cc_start: 0.9012 (mmm) cc_final: 0.8499 (tpp) REVERT: K 430 LYS cc_start: 0.8690 (tmmt) cc_final: 0.8154 (mmtm) REVERT: K 432 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.5891 (t80) REVERT: C 348 MET cc_start: 0.5826 (mpp) cc_final: 0.5570 (pmm) REVERT: C 402 ARG cc_start: 0.8233 (tpm170) cc_final: 0.7870 (ttp-170) REVERT: E 148 MET cc_start: 0.3541 (mmm) cc_final: 0.2893 (mmm) REVERT: E 217 LEU cc_start: 0.4407 (pt) cc_final: 0.3865 (mt) REVERT: E 230 MET cc_start: 0.3393 (OUTLIER) cc_final: 0.2685 (tpt) REVERT: E 420 TYR cc_start: 0.5190 (p90) cc_final: 0.4457 (p90) outliers start: 79 outliers final: 52 residues processed: 355 average time/residue: 0.6065 time to fit residues: 243.8901 Evaluate side-chains 348 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 283 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 83 HIS Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 318 ARG Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain K residue 219 ILE Chi-restraints excluded: chain K residue 239 THR Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain K residue 372 GLN Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 150 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 220 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 8 optimal weight: 0.1980 chunk 55 optimal weight: 0.8980 chunk 171 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 329 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 372 GLN ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5119 r_free = 0.5119 target = 0.211817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.135925 restraints weight = 26791.200| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 6.46 r_work: 0.3921 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.9820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 19582 Z= 0.160 Angle : 0.774 11.765 26564 Z= 0.395 Chirality : 0.047 0.408 2880 Planarity : 0.005 0.091 3461 Dihedral : 8.795 146.306 2682 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.42 % Rotamer: Outliers : 3.07 % Allowed : 29.28 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.17), residues: 2372 helix: 0.92 (0.15), residues: 1164 sheet: -0.96 (0.30), residues: 310 loop : -0.60 (0.22), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 282 TYR 0.028 0.001 TYR B 159 PHE 0.029 0.002 PHE A 49 TRP 0.029 0.002 TRP A 388 HIS 0.012 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00362 (19576) covalent geometry : angle 0.77048 (26561) hydrogen bonds : bond 0.04360 ( 976) hydrogen bonds : angle 4.93133 ( 2850) metal coordination : bond 0.00060 ( 4) Misc. bond : bond 0.01121 ( 1) link_TRANS : bond 0.05761 ( 1) link_TRANS : angle 7.35567 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9597.12 seconds wall clock time: 163 minutes 42.80 seconds (9822.80 seconds total)