Starting phenix.real_space_refine on Sat Jan 25 19:32:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z6s_14529/01_2025/7z6s_14529.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z6s_14529/01_2025/7z6s_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_2025/7z6s_14529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z6s_14529/01_2025/7z6s_14529.map" model { file = "/net/cci-nas-00/data/ceres_data/7z6s_14529/01_2025/7z6s_14529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z6s_14529/01_2025/7z6s_14529.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 12.87, per 1000 atoms: 0.67 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: 4.97 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.04 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: 6.76 Time building geometry restraints manager: 5.69 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 441 or resid 501 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: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 48.720 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.160 ------------------------------------------------------------------------------- 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 : 0.006 0.065 19576 Z= 0.409 Angle : 0.848 10.658 26561 Z= 0.544 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 : 15.45 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (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 TRP 0.030 0.003 TRP C 333 HIS 0.012 0.002 HIS C 343 PHE 0.020 0.002 PHE E 326 TYR 0.024 0.003 TYR E 370 ARG 0.019 0.001 ARG E 144 *********************** 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 : 1.954 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: A 16 ILE cc_start: 0.5506 (mt) cc_final: 0.5252 (mm) REVERT: A 182 VAL cc_start: 0.4924 (m) cc_final: 0.4691 (t) REVERT: A 413 MET cc_start: 0.7084 (ttm) cc_final: 0.6610 (ttm) REVERT: B 118 ASP cc_start: 0.7243 (m-30) cc_final: 0.7001 (m-30) REVERT: H 64 ILE cc_start: 0.6622 (mt) cc_final: 0.6370 (mt) REVERT: H 118 ASP cc_start: 0.6792 (m-30) cc_final: 0.6534 (m-30) REVERT: H 167 PHE cc_start: 0.5167 (m-80) cc_final: 0.4530 (m-10) REVERT: H 398 TYR cc_start: 0.6959 (m-80) cc_final: 0.6685 (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: 0.6982 (pp30) REVERT: K 154 MET cc_start: 0.8287 (mmm) cc_final: 0.8069 (mmm) REVERT: K 245 ASP cc_start: 0.7206 (t0) cc_final: 0.6857 (p0) REVERT: K 285 GLN cc_start: 0.7495 (pt0) cc_final: 0.6321 (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: 0.6523 (p) outliers start: 81 outliers final: 19 residues processed: 713 average time/residue: 1.2488 time to fit residues: 1005.8237 Evaluate side-chains 403 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 381 time to evaluate : 1.975 ------------------------------------------------------------------------------- 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 199 optimal weight: 10.0000 chunk 178 optimal weight: 20.0000 chunk 99 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 184 optimal weight: 20.0000 chunk 71 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 214 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 50 ASN ** 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 414 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 C 242 GLN C 265 ASN C 378 GLN E 242 GLN E 265 ASN E 343 HIS E 378 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5433 r_free = 0.5433 target = 0.253899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5100 r_free = 0.5100 target = 0.197390 restraints weight = 32142.677| |-----------------------------------------------------------------------------| r_work (start): 0.5002 rms_B_bonded: 3.65 r_work (final): 0.5002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5002 r_free = 0.5002 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5003 r_free = 0.5003 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.5003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 19576 Z= 0.244 Angle : 0.722 12.637 26561 Z= 0.380 Chirality : 0.046 0.218 2880 Planarity : 0.006 0.126 3461 Dihedral : 10.111 173.652 2713 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.91 % Favored : 97.01 % Rotamer: Outliers : 5.22 % Allowed : 17.81 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2372 helix: 0.82 (0.15), residues: 1196 sheet: -1.13 (0.30), residues: 294 loop : -0.96 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 21 HIS 0.011 0.001 HIS H 396 PHE 0.030 0.002 PHE A 138 TYR 0.027 0.002 TYR C 162 ARG 0.017 0.001 ARG C 259 *********************** 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 531 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 424 time to evaluate : 2.284 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: A 96 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7395 (ptpp) REVERT: A 141 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7535 (t80) REVERT: A 199 ASP cc_start: 0.7224 (m-30) cc_final: 0.6462 (m-30) REVERT: A 297 GLU cc_start: 0.7884 (tt0) cc_final: 0.7627 (mm-30) REVERT: A 413 MET cc_start: 0.7936 (ttm) cc_final: 0.7324 (ttm) REVERT: A 417 GLU cc_start: 0.7292 (tt0) cc_final: 0.6915 (tt0) REVERT: A 424 ASP cc_start: 0.8285 (m-30) cc_final: 0.8070 (m-30) REVERT: A 438 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7585 (p0) REVERT: B 64 ILE cc_start: 0.8201 (mp) cc_final: 0.7921 (mt) REVERT: B 118 ASP cc_start: 0.7551 (m-30) cc_final: 0.7304 (m-30) REVERT: B 122 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6948 (ttmt) REVERT: B 164 MET cc_start: 0.7404 (mtp) cc_final: 0.7181 (mtp) REVERT: B 167 PHE cc_start: 0.6990 (m-10) cc_final: 0.5726 (m-80) REVERT: B 209 ASP cc_start: 0.6270 (t0) cc_final: 0.5938 (t70) REVERT: B 306 ARG cc_start: 0.7896 (mtt180) cc_final: 0.7611 (mpt180) REVERT: B 363 MET cc_start: 0.6753 (ptt) cc_final: 0.6465 (pp-130) REVERT: H 65 LEU cc_start: 0.8277 (mp) cc_final: 0.8006 (mp) REVERT: H 136 THR cc_start: 0.7295 (m) cc_final: 0.6972 (p) REVERT: H 197 ASP cc_start: 0.8039 (m-30) cc_final: 0.7464 (m-30) REVERT: H 198 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: H 249 ASP cc_start: 0.6241 (OUTLIER) cc_final: 0.5889 (p0) REVERT: H 286 VAL cc_start: 0.6543 (t) cc_final: 0.6262 (t) REVERT: H 323 MET cc_start: 0.7728 (tpt) cc_final: 0.6945 (tpt) REVERT: H 333 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.6985 (mp) REVERT: H 412 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: K 154 MET cc_start: 0.8223 (mmm) cc_final: 0.7842 (mmm) REVERT: K 245 ASP cc_start: 0.7511 (t0) cc_final: 0.7221 (p0) REVERT: K 285 GLN cc_start: 0.7917 (pt0) cc_final: 0.6454 (mm-40) REVERT: K 304 LYS cc_start: 0.8750 (tppt) cc_final: 0.8384 (tppt) REVERT: K 313 MET cc_start: 0.5224 (mtp) cc_final: 0.4800 (tmm) REVERT: K 370 LYS cc_start: 0.8307 (tttp) cc_final: 0.7758 (tppt) REVERT: K 377 MET cc_start: 0.5916 (ttp) cc_final: 0.5632 (ttp) REVERT: E 144 ARG cc_start: 0.7515 (ttt90) cc_final: 0.7005 (tpt90) REVERT: E 145 PRO cc_start: 0.5313 (Cg_exo) cc_final: 0.4569 (Cg_endo) REVERT: E 329 GLN cc_start: 0.2817 (OUTLIER) cc_final: 0.2179 (pp30) REVERT: E 444 LEU cc_start: 0.7013 (mm) cc_final: 0.6729 (tp) outliers start: 107 outliers final: 27 residues processed: 485 average time/residue: 1.2693 time to fit residues: 699.3512 Evaluate side-chains 370 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 334 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 328 VAL Chi-restraints excluded: chain A residue 342 GLN 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 245 GLN Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 50 TYR 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 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 333 ILE Chi-restraints excluded: chain H residue 412 GLU Chi-restraints excluded: chain K residue 112 LYS Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain E residue 176 VAL 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 55 optimal weight: 10.0000 chunk 227 optimal weight: 20.0000 chunk 152 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 156 optimal weight: 0.0980 chunk 202 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 18 ASN A 35 GLN A 107 HIS A 256 GLN B 347 ASN H 8 GLN H 43 GLN ** H 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN ** H 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 ASN ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 309 HIS ** E 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5332 r_free = 0.5332 target = 0.239529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.156783 restraints weight = 30127.421| |-----------------------------------------------------------------------------| r_work (start): 0.4542 rms_B_bonded: 4.06 r_work: 0.4351 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.4351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4365 r_free = 0.4365 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4365 r_free = 0.4365 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.4365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 19576 Z= 0.301 Angle : 0.737 14.490 26561 Z= 0.383 Chirality : 0.046 0.245 2880 Planarity : 0.006 0.108 3461 Dihedral : 9.840 176.512 2687 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.71 % Favored : 96.21 % Rotamer: Outliers : 4.98 % Allowed : 20.94 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2372 helix: 0.78 (0.15), residues: 1212 sheet: -1.05 (0.30), residues: 322 loop : -0.88 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 21 HIS 0.013 0.001 HIS A 8 PHE 0.041 0.003 PHE B 167 TYR 0.026 0.002 TYR H 36 ARG 0.008 0.001 ARG H 380 *********************** 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: 102 poor density : 396 time to evaluate : 2.024 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 36 MET cc_start: 0.7238 (mtt) cc_final: 0.6725 (mpp) REVERT: A 76 ASP cc_start: 0.6759 (m-30) cc_final: 0.6134 (t0) REVERT: A 101 ASN cc_start: 0.7515 (OUTLIER) cc_final: 0.7045 (t0) REVERT: A 141 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7701 (t80) REVERT: A 202 PHE cc_start: 0.6510 (m-80) cc_final: 0.6200 (m-10) REVERT: A 276 ILE cc_start: 0.6647 (OUTLIER) cc_final: 0.6375 (pt) REVERT: A 297 GLU cc_start: 0.8457 (tt0) cc_final: 0.7758 (mm-30) REVERT: A 413 MET cc_start: 0.8235 (ttm) cc_final: 0.7764 (ttm) REVERT: A 417 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7321 (tt0) REVERT: A 424 ASP cc_start: 0.8378 (m-30) cc_final: 0.7927 (m-30) REVERT: B 122 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7307 (ttmt) REVERT: B 194 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6960 (mt-10) REVERT: H 50 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7547 (m-10) REVERT: H 129 CYS cc_start: 0.7883 (t) cc_final: 0.7267 (p) REVERT: H 159 TYR cc_start: 0.8403 (m-80) cc_final: 0.8059 (m-80) REVERT: H 198 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: H 323 MET cc_start: 0.8080 (tpt) cc_final: 0.7508 (tpp) REVERT: H 363 MET cc_start: 0.6588 (pp-130) cc_final: 0.5944 (ppp) REVERT: H 368 ILE cc_start: 0.7095 (mm) cc_final: 0.6883 (mt) REVERT: H 381 ILE cc_start: 0.8168 (tp) cc_final: 0.7963 (tp) REVERT: K 192 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.6770 (p-80) REVERT: K 245 ASP cc_start: 0.8146 (t0) cc_final: 0.7714 (p0) REVERT: K 251 ASP cc_start: 0.8045 (p0) cc_final: 0.7769 (p0) REVERT: K 285 GLN cc_start: 0.8113 (pt0) cc_final: 0.6867 (mm-40) REVERT: K 304 LYS cc_start: 0.8909 (tppt) cc_final: 0.8415 (tppt) REVERT: K 309 HIS cc_start: 0.7389 (m170) cc_final: 0.6975 (m-70) REVERT: K 344 VAL cc_start: 0.8062 (m) cc_final: 0.7754 (m) REVERT: K 370 LYS cc_start: 0.8445 (tttp) cc_final: 0.7739 (tppt) REVERT: K 372 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7250 (pm20) REVERT: K 377 MET cc_start: 0.7026 (ttp) cc_final: 0.6774 (ttp) REVERT: K 384 ILE cc_start: 0.7593 (tp) cc_final: 0.6929 (tt) REVERT: K 388 TRP cc_start: 0.8087 (m100) cc_final: 0.7883 (m100) REVERT: K 417 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8320 (tm-30) REVERT: K 424 ASP cc_start: 0.8144 (t70) cc_final: 0.7602 (m-30) REVERT: E 148 MET cc_start: 0.3881 (mmm) cc_final: 0.3597 (mmm) REVERT: E 329 GLN cc_start: 0.2758 (OUTLIER) cc_final: 0.2198 (pp30) REVERT: E 348 MET cc_start: 0.4126 (mpp) cc_final: 0.3920 (mpp) REVERT: E 444 LEU cc_start: 0.7045 (mm) cc_final: 0.6812 (tp) outliers start: 102 outliers final: 34 residues processed: 457 average time/residue: 1.1956 time to fit residues: 621.5146 Evaluate side-chains 365 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 321 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU 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 276 ILE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 122 LYS 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 178 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain H residue 3 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 168 SER 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 255 VAL Chi-restraints excluded: chain H residue 318 ARG Chi-restraints excluded: chain H residue 385 PHE Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain K residue 112 LYS Chi-restraints excluded: chain K residue 147 SER Chi-restraints excluded: chain K residue 192 HIS Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 372 GLN Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain K residue 429 GLU 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 329 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 225 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 171 optimal weight: 50.0000 chunk 169 optimal weight: 1.9990 chunk 223 optimal weight: 50.0000 chunk 155 optimal weight: 1.9990 chunk 183 optimal weight: 40.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN A 50 ASN A 256 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 ASN ** H 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 HIS ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 HIS ** K 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 256 GLN ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 434 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5177 r_free = 0.5177 target = 0.207534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.139799 restraints weight = 26584.552| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 4.10 r_work: 0.4039 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.7980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 19576 Z= 0.420 Angle : 0.858 12.748 26561 Z= 0.446 Chirality : 0.051 0.233 2880 Planarity : 0.006 0.101 3461 Dihedral : 9.920 145.224 2685 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 6.54 % Allowed : 21.28 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2372 helix: 0.49 (0.14), residues: 1194 sheet: -0.89 (0.31), residues: 288 loop : -1.10 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 346 HIS 0.016 0.002 HIS A 8 PHE 0.053 0.003 PHE H 385 TYR 0.023 0.002 TYR C 162 ARG 0.012 0.001 ARG H 320 *********************** 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 532 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 398 time to evaluate : 2.191 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: A 2 ARG cc_start: 0.6507 (ptp90) cc_final: 0.5999 (ptm160) REVERT: A 53 PHE cc_start: 0.7263 (m-10) cc_final: 0.7061 (m-80) REVERT: A 101 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.8094 (t0) REVERT: A 113 GLU cc_start: 0.8226 (mp0) cc_final: 0.7923 (mp0) REVERT: A 114 ILE cc_start: 0.8884 (pt) cc_final: 0.8662 (pt) REVERT: A 123 ARG cc_start: 0.8598 (ttp-110) cc_final: 0.8004 (tmm160) REVERT: A 125 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8802 (mp) REVERT: A 141 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.7938 (t80) REVERT: A 176 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8546 (mp10) REVERT: A 203 MET cc_start: 0.6946 (mmm) cc_final: 0.6579 (mmt) REVERT: A 297 GLU cc_start: 0.8400 (tt0) cc_final: 0.8176 (mm-30) REVERT: A 300 ASN cc_start: 0.8077 (t0) cc_final: 0.7716 (t0) REVERT: A 304 LYS cc_start: 0.8327 (tppt) cc_final: 0.8093 (tptt) REVERT: A 417 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: A 424 ASP cc_start: 0.8629 (m-30) cc_final: 0.8085 (m-30) REVERT: B 156 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7959 (ttm-80) REVERT: B 158 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7850 (mm-30) REVERT: B 164 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.6983 (mtm) REVERT: B 194 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7301 (mt-10) REVERT: B 213 ARG cc_start: 0.7319 (ptp-170) cc_final: 0.6998 (ptp-170) REVERT: B 359 ARG cc_start: 0.8061 (mmm160) cc_final: 0.7426 (tmm160) REVERT: B 363 MET cc_start: 0.7533 (pp-130) cc_final: 0.7085 (pp-130) REVERT: B 390 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8335 (ttm170) REVERT: H 35 ASN cc_start: 0.7852 (p0) cc_final: 0.7238 (p0) REVERT: H 50 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.8288 (m-10) REVERT: H 147 MET cc_start: 0.8614 (mmm) cc_final: 0.8273 (mmm) REVERT: H 192 LEU cc_start: 0.8728 (mt) cc_final: 0.8472 (mt) REVERT: H 198 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: H 233 MET cc_start: 0.6497 (mmp) cc_final: 0.6292 (mmm) REVERT: H 281 TYR cc_start: 0.7140 (m-10) cc_final: 0.6116 (t80) REVERT: H 293 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.7050 (mtt) REVERT: H 318 ARG cc_start: 0.6426 (OUTLIER) cc_final: 0.5687 (mtm180) REVERT: H 336 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8129 (mttp) REVERT: H 388 MET cc_start: 0.7394 (tpp) cc_final: 0.7176 (mmp) REVERT: K 91 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.6901 (pt0) REVERT: K 176 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8327 (mm-40) REVERT: K 215 ARG cc_start: 0.6721 (ttm110) cc_final: 0.6463 (mtp-110) REVERT: K 221 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7467 (mtt-85) REVERT: K 304 LYS cc_start: 0.8804 (tppt) cc_final: 0.8475 (tppt) REVERT: K 357 TYR cc_start: 0.8126 (m-10) cc_final: 0.7907 (m-80) REVERT: K 370 LYS cc_start: 0.8113 (tttp) cc_final: 0.7745 (tppt) REVERT: K 424 ASP cc_start: 0.8491 (t70) cc_final: 0.8081 (m-30) REVERT: C 253 MET cc_start: 0.4979 (OUTLIER) cc_final: 0.4774 (mmm) REVERT: C 348 MET cc_start: 0.4673 (pmm) cc_final: 0.4355 (pp-130) REVERT: E 144 ARG cc_start: 0.7845 (ttt90) cc_final: 0.7431 (tpt90) REVERT: E 348 MET cc_start: 0.4785 (mpp) cc_final: 0.4465 (mpp) outliers start: 134 outliers final: 39 residues processed: 488 average time/residue: 1.3128 time to fit residues: 725.1432 Evaluate side-chains 365 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 309 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 125 LEU 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 251 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain B residue 135 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 164 MET Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 255 VAL 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 50 TYR Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain H residue 161 ASP 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 255 VAL Chi-restraints excluded: chain H residue 257 MET Chi-restraints excluded: chain H residue 274 THR Chi-restraints excluded: chain H residue 293 MET Chi-restraints excluded: chain H residue 318 ARG Chi-restraints excluded: chain H residue 336 LYS Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 176 GLN Chi-restraints excluded: chain K residue 219 ILE Chi-restraints excluded: chain K residue 221 ARG Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 318 LEU Chi-restraints excluded: chain K residue 439 SER Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain E residue 176 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 44 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 chunk 199 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN B 105 HIS ** B 307 HIS ** 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 245 GLN ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN K 107 HIS K 186 ASN K 206 ASN ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN C 159 HIS C 343 HIS E 242 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5182 r_free = 0.5182 target = 0.208697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.138351 restraints weight = 26505.133| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 5.34 r_work: 0.4026 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.8367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19576 Z= 0.243 Angle : 0.724 10.894 26561 Z= 0.372 Chirality : 0.046 0.263 2880 Planarity : 0.005 0.090 3461 Dihedral : 9.352 143.090 2681 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.33 % Favored : 96.59 % Rotamer: Outliers : 4.78 % Allowed : 24.74 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2372 helix: 0.73 (0.15), residues: 1196 sheet: -0.96 (0.31), residues: 300 loop : -0.77 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 21 HIS 0.016 0.001 HIS E 322 PHE 0.031 0.002 PHE H 385 TYR 0.016 0.001 TYR B 310 ARG 0.012 0.001 ARG A 390 *********************** 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 436 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 338 time to evaluate : 2.058 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 2 ARG cc_start: 0.6609 (ptp90) cc_final: 0.6228 (ptm160) REVERT: A 75 ILE cc_start: 0.8468 (mm) cc_final: 0.8006 (mt) REVERT: A 101 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7683 (t0) REVERT: A 113 GLU cc_start: 0.7834 (mp0) cc_final: 0.7586 (mp0) REVERT: A 123 ARG cc_start: 0.8497 (ttp-110) cc_final: 0.7981 (tmm160) REVERT: A 141 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7434 (t80) REVERT: A 155 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7541 (mm-30) REVERT: A 176 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8803 (mp10) REVERT: A 192 HIS cc_start: 0.7876 (t-90) cc_final: 0.7665 (t-170) REVERT: A 203 MET cc_start: 0.6971 (mmm) cc_final: 0.6734 (mmt) REVERT: A 297 GLU cc_start: 0.8387 (tt0) cc_final: 0.8100 (mm-30) REVERT: A 300 ASN cc_start: 0.7910 (t0) cc_final: 0.7543 (t160) REVERT: A 417 GLU cc_start: 0.7926 (tt0) cc_final: 0.7673 (tt0) REVERT: B 58 LYS cc_start: 0.2141 (pttt) cc_final: 0.1846 (ttpt) REVERT: B 156 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8028 (ttm-80) REVERT: B 284 LEU cc_start: 0.8193 (pt) cc_final: 0.7868 (tm) REVERT: B 299 MET cc_start: 0.7430 (mtt) cc_final: 0.7184 (mtt) REVERT: B 359 ARG cc_start: 0.8137 (mmm160) cc_final: 0.7253 (tmm160) REVERT: B 363 MET cc_start: 0.7590 (pp-130) cc_final: 0.7026 (pp-130) REVERT: B 390 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8126 (ttm170) REVERT: H 35 ASN cc_start: 0.7905 (p0) cc_final: 0.7308 (p0) REVERT: H 50 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.8117 (m-10) REVERT: H 147 MET cc_start: 0.8424 (mmm) cc_final: 0.8137 (mmt) REVERT: H 191 GLN cc_start: 0.7997 (mm110) cc_final: 0.7687 (mm-40) REVERT: H 192 LEU cc_start: 0.8777 (mt) cc_final: 0.8560 (mt) REVERT: H 240 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7312 (pt) REVERT: H 336 LYS cc_start: 0.8689 (pptt) cc_final: 0.8487 (pptt) REVERT: H 388 MET cc_start: 0.6634 (tpp) cc_final: 0.6397 (mmt) REVERT: K 154 MET cc_start: 0.8597 (mmm) cc_final: 0.8334 (mmm) REVERT: K 285 GLN cc_start: 0.7979 (pm20) cc_final: 0.7388 (mm-40) REVERT: K 304 LYS cc_start: 0.8757 (tppt) cc_final: 0.8368 (tppt) REVERT: K 370 LYS cc_start: 0.8265 (tttp) cc_final: 0.8033 (tptt) REVERT: K 377 MET cc_start: 0.7339 (ttp) cc_final: 0.7048 (ttp) REVERT: K 388 TRP cc_start: 0.8010 (m100) cc_final: 0.7713 (m100) REVERT: K 424 ASP cc_start: 0.8460 (t70) cc_final: 0.8148 (m-30) REVERT: K 425 MET cc_start: 0.8841 (mmm) cc_final: 0.8252 (tpp) REVERT: K 430 LYS cc_start: 0.8619 (ttpt) cc_final: 0.7990 (mmtt) REVERT: K 432 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.5408 (t80) REVERT: E 144 ARG cc_start: 0.7797 (ttt90) cc_final: 0.7302 (tpt90) REVERT: E 348 MET cc_start: 0.4915 (mpp) cc_final: 0.4710 (mpp) outliers start: 98 outliers final: 40 residues processed: 412 average time/residue: 1.2540 time to fit residues: 586.1511 Evaluate side-chains 352 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 303 time to evaluate : 2.053 ------------------------------------------------------------------------------- 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 141 PHE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 237 THR 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 30 ILE 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 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 240 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 318 ARG Chi-restraints excluded: chain H residue 354 CYS Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 219 ILE Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 439 SER Chi-restraints excluded: chain C residue 157 GLN 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 209 GLU Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 284 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 24 optimal weight: 0.9990 chunk 201 optimal weight: 50.0000 chunk 234 optimal weight: 40.0000 chunk 37 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 16 optimal weight: 0.0170 chunk 187 optimal weight: 20.0000 chunk 193 optimal weight: 50.0000 chunk 185 optimal weight: 10.0000 chunk 204 optimal weight: 40.0000 chunk 159 optimal weight: 0.6980 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN A 216 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 HIS ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN H 245 GLN H 247 ASN ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 GLN ** K 139 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5123 r_free = 0.5123 target = 0.203235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.125286 restraints weight = 26228.034| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 4.01 r_work: 0.3934 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.8917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 19576 Z= 0.340 Angle : 0.741 12.119 26561 Z= 0.382 Chirality : 0.047 0.203 2880 Planarity : 0.005 0.086 3461 Dihedral : 9.346 144.895 2681 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.01 % Favored : 95.91 % Rotamer: Outliers : 5.17 % Allowed : 24.94 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.17), residues: 2372 helix: 0.77 (0.15), residues: 1182 sheet: -1.26 (0.30), residues: 312 loop : -0.64 (0.22), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 388 HIS 0.012 0.002 HIS B 190 PHE 0.026 0.003 PHE A 138 TYR 0.021 0.002 TYR A 83 ARG 0.008 0.001 ARG H 282 *********************** 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 423 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 317 time to evaluate : 2.087 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 35 GLN cc_start: 0.6890 (OUTLIER) cc_final: 0.6664 (mp10) REVERT: A 75 ILE cc_start: 0.8737 (mm) cc_final: 0.8379 (mt) REVERT: A 101 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7816 (t0) REVERT: A 123 ARG cc_start: 0.8501 (ttp-110) cc_final: 0.7906 (tmm160) REVERT: A 133 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7659 (mt0) REVERT: A 141 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7365 (t80) REVERT: A 176 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8749 (mp10) REVERT: A 300 ASN cc_start: 0.7636 (t0) cc_final: 0.7172 (t160) REVERT: A 417 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: B 58 LYS cc_start: 0.2875 (pttt) cc_final: 0.2342 (tmmt) REVERT: B 156 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7986 (ttm-80) REVERT: B 299 MET cc_start: 0.7406 (mtt) cc_final: 0.7078 (mtt) REVERT: B 359 ARG cc_start: 0.8105 (mmm160) cc_final: 0.7494 (tmm160) REVERT: B 363 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.6937 (pp-130) REVERT: H 25 SER cc_start: 0.8002 (t) cc_final: 0.7795 (m) REVERT: H 50 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.8218 (m-10) REVERT: H 147 MET cc_start: 0.8535 (mmm) cc_final: 0.8283 (mmt) REVERT: H 163 ILE cc_start: 0.8410 (tp) cc_final: 0.8146 (tp) REVERT: H 191 GLN cc_start: 0.7931 (mm110) cc_final: 0.7659 (mm-40) REVERT: H 192 LEU cc_start: 0.8822 (mt) cc_final: 0.8605 (mt) REVERT: H 198 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: H 240 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7654 (pt) REVERT: H 279 GLN cc_start: 0.7578 (pm20) cc_final: 0.7337 (pm20) REVERT: H 288 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6341 (tp30) REVERT: H 306 ARG cc_start: 0.8574 (mpt-90) cc_final: 0.8354 (mpt-90) REVERT: H 318 ARG cc_start: 0.6707 (OUTLIER) cc_final: 0.6319 (mtp85) REVERT: H 375 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8435 (pp30) REVERT: H 388 MET cc_start: 0.6894 (tpp) cc_final: 0.6692 (mmt) REVERT: K 120 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7602 (m-30) REVERT: K 176 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8399 (mm-40) REVERT: K 285 GLN cc_start: 0.8035 (pm20) cc_final: 0.7390 (mm-40) REVERT: K 370 LYS cc_start: 0.8223 (tttp) cc_final: 0.7971 (tptt) REVERT: K 377 MET cc_start: 0.7344 (ttp) cc_final: 0.7047 (ttp) REVERT: K 388 TRP cc_start: 0.7928 (m100) cc_final: 0.7561 (m100) REVERT: K 424 ASP cc_start: 0.8461 (t70) cc_final: 0.8073 (m-30) REVERT: K 425 MET cc_start: 0.8862 (mmm) cc_final: 0.8161 (tpp) REVERT: K 430 LYS cc_start: 0.8396 (ttpt) cc_final: 0.7901 (mmtt) REVERT: K 432 TYR cc_start: 0.7567 (OUTLIER) cc_final: 0.5290 (t80) REVERT: E 148 MET cc_start: 0.3935 (mmm) cc_final: 0.3579 (mmm) outliers start: 106 outliers final: 50 residues processed: 396 average time/residue: 1.2877 time to fit residues: 586.0820 Evaluate side-chains 367 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 300 time to evaluate : 2.250 ------------------------------------------------------------------------------- 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 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 239 THR 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 49 VAL 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 178 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 30 ILE 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 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 249 ASP Chi-restraints excluded: chain H residue 274 THR Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 318 ARG Chi-restraints excluded: chain H residue 354 CYS Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 176 GLN Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain K residue 219 ILE Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 439 SER 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 209 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 43 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 118 optimal weight: 0.0170 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 225 optimal weight: 20.0000 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 ASN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS E 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5140 r_free = 0.5140 target = 0.205104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.128875 restraints weight = 26320.950| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 3.46 r_work: 0.3980 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.9089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19576 Z= 0.245 Angle : 0.718 14.334 26561 Z= 0.366 Chirality : 0.046 0.325 2880 Planarity : 0.005 0.089 3461 Dihedral : 9.119 144.034 2681 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 4.44 % Allowed : 26.21 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2372 helix: 0.86 (0.15), residues: 1188 sheet: -1.22 (0.29), residues: 326 loop : -0.61 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 388 HIS 0.013 0.001 HIS A 192 PHE 0.026 0.002 PHE B 212 TYR 0.023 0.001 TYR B 159 ARG 0.005 0.000 ARG H 282 *********************** 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 413 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 322 time to evaluate : 2.393 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 75 ILE cc_start: 0.8720 (mm) cc_final: 0.8384 (mt) REVERT: A 101 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7781 (t0) REVERT: A 123 ARG cc_start: 0.8428 (ttp-110) cc_final: 0.8016 (tmm160) REVERT: A 176 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8769 (mp10) REVERT: A 300 ASN cc_start: 0.7397 (t0) cc_final: 0.6897 (t160) REVERT: A 367 ASP cc_start: 0.6174 (OUTLIER) cc_final: 0.4500 (t0) REVERT: A 397 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8599 (tp) REVERT: A 417 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: A 424 ASP cc_start: 0.8079 (m-30) cc_final: 0.7839 (m-30) REVERT: B 58 LYS cc_start: 0.2997 (pttt) cc_final: 0.2558 (tmmt) REVERT: B 156 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.8002 (ttm-80) REVERT: B 299 MET cc_start: 0.7396 (mtt) cc_final: 0.7092 (mtt) REVERT: B 359 ARG cc_start: 0.8000 (mmm160) cc_final: 0.7462 (tmm160) REVERT: B 363 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6908 (pp-130) REVERT: H 50 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.8132 (m-10) REVERT: H 66 VAL cc_start: 0.8444 (p) cc_final: 0.8149 (p) REVERT: H 134 GLN cc_start: 0.7256 (pp30) cc_final: 0.6807 (pp30) REVERT: H 147 MET cc_start: 0.8415 (mmm) cc_final: 0.8166 (mmt) REVERT: H 163 ILE cc_start: 0.8395 (tp) cc_final: 0.8073 (pp) REVERT: H 191 GLN cc_start: 0.7981 (mm110) cc_final: 0.7753 (mm-40) REVERT: H 192 LEU cc_start: 0.8773 (mt) cc_final: 0.8562 (mt) REVERT: H 299 MET cc_start: 0.6948 (pmm) cc_final: 0.5611 (mmt) REVERT: H 318 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.6279 (mtp85) REVERT: H 336 LYS cc_start: 0.8705 (pptt) cc_final: 0.8185 (mttp) REVERT: H 375 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8452 (pp30) REVERT: H 388 MET cc_start: 0.6887 (tpp) cc_final: 0.6678 (mmt) REVERT: K 112 LYS cc_start: 0.8465 (pttt) cc_final: 0.8065 (pttt) REVERT: K 176 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8387 (mm-40) REVERT: K 285 GLN cc_start: 0.7889 (pm20) cc_final: 0.7346 (mm-40) REVERT: K 370 LYS cc_start: 0.8251 (tttp) cc_final: 0.7992 (tptt) REVERT: K 377 MET cc_start: 0.7286 (ttp) cc_final: 0.7014 (ttp) REVERT: K 388 TRP cc_start: 0.7885 (m100) cc_final: 0.7531 (m100) REVERT: K 424 ASP cc_start: 0.8476 (t70) cc_final: 0.8169 (m-30) REVERT: K 425 MET cc_start: 0.8861 (mmm) cc_final: 0.8362 (tpp) REVERT: K 430 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8011 (mmtt) REVERT: K 432 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.5566 (t80) REVERT: C 348 MET cc_start: 0.4691 (pmm) cc_final: 0.4480 (pmm) REVERT: E 144 ARG cc_start: 0.7718 (ttt90) cc_final: 0.7133 (tpt90) outliers start: 91 outliers final: 40 residues processed: 391 average time/residue: 1.2603 time to fit residues: 558.4660 Evaluate side-chains 351 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 299 time to evaluate : 2.031 ------------------------------------------------------------------------------- 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 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 269 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 TYR 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 164 MET Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 318 ARG Chi-restraints excluded: chain H residue 354 CYS Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 176 GLN 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 248 LEU Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 432 TYR 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 209 GLU Chi-restraints excluded: chain E residue 261 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 207 optimal weight: 40.0000 chunk 107 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 212 optimal weight: 40.0000 chunk 148 optimal weight: 0.2980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5127 r_free = 0.5127 target = 0.204212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.127750 restraints weight = 26249.957| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 3.61 r_work: 0.3949 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.9371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19576 Z= 0.275 Angle : 0.737 11.228 26561 Z= 0.376 Chirality : 0.047 0.263 2880 Planarity : 0.005 0.089 3461 Dihedral : 9.085 144.576 2681 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.92 % Favored : 96.04 % Rotamer: Outliers : 4.39 % Allowed : 26.65 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.17), residues: 2372 helix: 0.79 (0.15), residues: 1190 sheet: -1.19 (0.30), residues: 306 loop : -0.57 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 333 HIS 0.014 0.001 HIS C 429 PHE 0.038 0.002 PHE H 385 TYR 0.040 0.002 TYR E 393 ARG 0.014 0.000 ARG C 427 *********************** 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 401 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 311 time to evaluate : 2.026 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 35 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6899 (mp10) REVERT: A 75 ILE cc_start: 0.8678 (mm) cc_final: 0.8376 (mt) REVERT: A 101 ASN cc_start: 0.8156 (OUTLIER) cc_final: 0.7874 (t0) REVERT: A 123 ARG cc_start: 0.8441 (ttp-110) cc_final: 0.8011 (tmm160) REVERT: A 176 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8726 (mp10) REVERT: B 58 LYS cc_start: 0.3092 (pttt) cc_final: 0.2644 (tmmt) REVERT: B 64 ILE cc_start: 0.8839 (mp) cc_final: 0.8573 (mp) REVERT: B 81 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.5882 (t80) REVERT: B 89 ASN cc_start: 0.7127 (m110) cc_final: 0.6774 (m-40) REVERT: B 156 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7917 (ttm-80) REVERT: B 279 GLN cc_start: 0.8041 (pm20) cc_final: 0.7660 (pm20) REVERT: B 299 MET cc_start: 0.7410 (mtt) cc_final: 0.7102 (mtt) REVERT: B 330 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7296 (tmm) REVERT: B 336 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8358 (mmtm) REVERT: B 359 ARG cc_start: 0.7998 (mmm160) cc_final: 0.7637 (tmm160) REVERT: B 363 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.6925 (pp-130) REVERT: H 50 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.8174 (m-10) REVERT: H 163 ILE cc_start: 0.8389 (tp) cc_final: 0.8136 (pp) REVERT: H 191 GLN cc_start: 0.8089 (mm110) cc_final: 0.7836 (mm-40) REVERT: H 192 LEU cc_start: 0.8772 (mt) cc_final: 0.8553 (mt) REVERT: H 207 LEU cc_start: 0.7827 (mm) cc_final: 0.7306 (mm) REVERT: H 318 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.6292 (mtp180) REVERT: H 336 LYS cc_start: 0.8801 (pptt) cc_final: 0.8237 (mttp) REVERT: H 375 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8450 (pp30) REVERT: H 388 MET cc_start: 0.6867 (tpp) cc_final: 0.6572 (mmt) REVERT: K 60 LYS cc_start: 0.7676 (tptt) cc_final: 0.6555 (ttpt) REVERT: K 112 LYS cc_start: 0.8394 (pttt) cc_final: 0.8083 (pttt) REVERT: K 176 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8389 (mm-40) REVERT: K 285 GLN cc_start: 0.7962 (pm20) cc_final: 0.7437 (mm-40) REVERT: K 304 LYS cc_start: 0.8481 (tppt) cc_final: 0.8135 (tppt) REVERT: K 370 LYS cc_start: 0.8217 (tttp) cc_final: 0.7700 (tppt) REVERT: K 424 ASP cc_start: 0.8470 (t70) cc_final: 0.8185 (m-30) REVERT: K 425 MET cc_start: 0.8882 (mmm) cc_final: 0.8380 (tpp) REVERT: K 430 LYS cc_start: 0.8537 (ttpt) cc_final: 0.8024 (mmtt) REVERT: K 432 TYR cc_start: 0.7723 (OUTLIER) cc_final: 0.5698 (t80) REVERT: E 148 MET cc_start: 0.4094 (mmm) cc_final: 0.3787 (mmm) outliers start: 90 outliers final: 49 residues processed: 379 average time/residue: 1.2270 time to fit residues: 528.9069 Evaluate side-chains 353 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 291 time to evaluate : 2.073 ------------------------------------------------------------------------------- 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 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 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 269 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 156 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 330 MET Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 50 TYR 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 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 217 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 318 ARG Chi-restraints excluded: chain H residue 354 CYS Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 176 GLN 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 248 LEU Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 332 ILE 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 301 GLU Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 261 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 121 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 chunk 212 optimal weight: 40.0000 chunk 222 optimal weight: 6.9990 chunk 224 optimal weight: 50.0000 chunk 62 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 ASN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5088 r_free = 0.5088 target = 0.199598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.129348 restraints weight = 26052.320| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 3.99 r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.9869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 19576 Z= 0.411 Angle : 0.837 16.361 26561 Z= 0.429 Chirality : 0.050 0.269 2880 Planarity : 0.006 0.088 3461 Dihedral : 9.317 146.239 2681 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.17 % Favored : 95.78 % Rotamer: Outliers : 4.20 % Allowed : 27.57 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2372 helix: 0.69 (0.15), residues: 1188 sheet: -1.40 (0.30), residues: 318 loop : -0.57 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 346 HIS 0.013 0.002 HIS A 8 PHE 0.033 0.003 PHE H 20 TYR 0.034 0.002 TYR E 393 ARG 0.007 0.001 ARG B 213 *********************** 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 401 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 315 time to evaluate : 2.112 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 22 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6386 (tp30) REVERT: A 77 GLU cc_start: 0.7832 (pt0) cc_final: 0.7429 (pp20) REVERT: A 149 PHE cc_start: 0.7829 (m-80) cc_final: 0.7585 (m-80) REVERT: A 176 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8536 (mp10) REVERT: A 285 GLN cc_start: 0.8282 (pt0) cc_final: 0.7593 (mm110) REVERT: A 300 ASN cc_start: 0.7387 (t0) cc_final: 0.6997 (t0) REVERT: B 58 LYS cc_start: 0.2965 (pttt) cc_final: 0.2640 (ttpt) REVERT: B 81 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7093 (t80) REVERT: B 89 ASN cc_start: 0.7375 (m110) cc_final: 0.7171 (m-40) REVERT: B 245 GLN cc_start: 0.7904 (tt0) cc_final: 0.7649 (tp40) REVERT: B 299 MET cc_start: 0.7042 (mtt) cc_final: 0.6762 (mtt) REVERT: B 359 ARG cc_start: 0.8067 (mmm160) cc_final: 0.7734 (tmm160) REVERT: B 363 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.6759 (pp-130) REVERT: H 163 ILE cc_start: 0.8343 (tp) cc_final: 0.8031 (pp) REVERT: H 191 GLN cc_start: 0.7754 (mm110) cc_final: 0.7546 (mm-40) REVERT: H 192 LEU cc_start: 0.8732 (mt) cc_final: 0.8450 (mt) REVERT: H 299 MET cc_start: 0.6379 (pmm) cc_final: 0.5521 (mmt) REVERT: H 306 ARG cc_start: 0.8511 (mpt-90) cc_final: 0.8251 (mpt-90) REVERT: H 318 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6421 (mtp180) REVERT: H 327 ASP cc_start: 0.7721 (m-30) cc_final: 0.7507 (t0) REVERT: H 336 LYS cc_start: 0.8884 (pptt) cc_final: 0.8398 (mttp) REVERT: H 375 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8405 (pp30) REVERT: K 1 MET cc_start: 0.7629 (tmt) cc_final: 0.7306 (tmm) REVERT: K 101 ASN cc_start: 0.8502 (m-40) cc_final: 0.8104 (m-40) REVERT: K 112 LYS cc_start: 0.8244 (pttt) cc_final: 0.8011 (pttt) REVERT: K 176 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8404 (mm-40) REVERT: K 211 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7642 (t70) REVERT: K 280 LYS cc_start: 0.0773 (tptt) cc_final: 0.0394 (tptt) REVERT: K 304 LYS cc_start: 0.8539 (tppt) cc_final: 0.8084 (tppt) REVERT: K 370 LYS cc_start: 0.7927 (tttp) cc_final: 0.7671 (tptt) REVERT: K 377 MET cc_start: 0.7154 (ttp) cc_final: 0.6695 (ttp) REVERT: K 384 ILE cc_start: 0.8186 (pp) cc_final: 0.7452 (tt) REVERT: K 388 TRP cc_start: 0.8139 (m100) cc_final: 0.7694 (m100) REVERT: K 417 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8296 (tp30) REVERT: K 424 ASP cc_start: 0.8575 (t70) cc_final: 0.8356 (m-30) REVERT: K 425 MET cc_start: 0.8860 (mmm) cc_final: 0.8353 (tpp) REVERT: K 430 LYS cc_start: 0.8826 (ttpt) cc_final: 0.8351 (mmtt) REVERT: C 157 GLN cc_start: 0.6527 (pm20) cc_final: 0.6274 (tm-30) REVERT: C 259 ARG cc_start: 0.0779 (ttm170) cc_final: 0.0126 (tpp80) REVERT: E 217 LEU cc_start: 0.5175 (pt) cc_final: 0.4136 (mp) outliers start: 86 outliers final: 49 residues processed: 378 average time/residue: 1.2473 time to fit residues: 535.1554 Evaluate side-chains 343 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 286 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 82 THR 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 239 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 81 PHE 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 178 THR 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 381 ILE 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 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 179 VAL Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 318 ARG Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 354 CYS Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 176 GLN 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 257 THR Chi-restraints excluded: chain K residue 287 SER 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 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 209 GLU Chi-restraints excluded: chain E residue 261 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 27 optimal weight: 3.9990 chunk 173 optimal weight: 0.0970 chunk 98 optimal weight: 0.9990 chunk 8 optimal weight: 0.0470 chunk 223 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 307 HIS ** 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 307 HIS ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 ASN ** K 301 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 = 0.5088 r_free = 0.5088 target = 0.208909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.134686 restraints weight = 26229.874| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 5.42 r_work: 0.3891 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.9945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19576 Z= 0.238 Angle : 0.785 16.282 26561 Z= 0.398 Chirality : 0.047 0.359 2880 Planarity : 0.005 0.089 3461 Dihedral : 8.973 144.111 2681 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.42 % Rotamer: Outliers : 2.83 % Allowed : 29.97 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2372 helix: 0.79 (0.15), residues: 1180 sheet: -1.11 (0.31), residues: 302 loop : -0.65 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 388 HIS 0.011 0.001 HIS H 307 PHE 0.030 0.002 PHE H 385 TYR 0.031 0.001 TYR E 393 ARG 0.007 0.000 ARG H 282 ********************** 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 377 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 319 time to evaluate : 2.124 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 22 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6751 (pm20) REVERT: A 74 VAL cc_start: 0.7634 (p) cc_final: 0.7423 (t) REVERT: A 77 GLU cc_start: 0.7761 (pt0) cc_final: 0.7359 (pp20) REVERT: A 149 PHE cc_start: 0.8080 (m-80) cc_final: 0.7877 (m-80) REVERT: A 176 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8475 (mp10) REVERT: A 285 GLN cc_start: 0.8175 (pt0) cc_final: 0.7566 (mm110) REVERT: B 58 LYS cc_start: 0.3370 (pttt) cc_final: 0.2894 (tmmt) REVERT: B 81 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7420 (t80) REVERT: B 89 ASN cc_start: 0.7378 (m110) cc_final: 0.7058 (m-40) REVERT: B 155 VAL cc_start: 0.7808 (t) cc_final: 0.7580 (m) REVERT: B 156 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7779 (ttm-80) REVERT: B 245 GLN cc_start: 0.8193 (tt0) cc_final: 0.7972 (tp40) REVERT: B 279 GLN cc_start: 0.8123 (pm20) cc_final: 0.7842 (pm20) REVERT: B 299 MET cc_start: 0.7505 (mtt) cc_final: 0.7278 (mtt) REVERT: B 330 MET cc_start: 0.7608 (tpp) cc_final: 0.7145 (tmm) REVERT: B 359 ARG cc_start: 0.8191 (mmm160) cc_final: 0.7623 (pmt-80) REVERT: B 363 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.6831 (pp-130) REVERT: H 66 VAL cc_start: 0.8398 (p) cc_final: 0.8158 (p) REVERT: H 86 ARG cc_start: 0.6663 (tpt170) cc_final: 0.6061 (mmt-90) REVERT: H 163 ILE cc_start: 0.8338 (tp) cc_final: 0.8063 (pp) REVERT: H 192 LEU cc_start: 0.8698 (mt) cc_final: 0.8451 (mt) REVERT: H 299 MET cc_start: 0.7178 (pmm) cc_final: 0.5996 (mmt) REVERT: H 318 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6147 (mtp180) REVERT: H 336 LYS cc_start: 0.8884 (pptt) cc_final: 0.8269 (mmtm) REVERT: H 375 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8532 (pp30) REVERT: K 1 MET cc_start: 0.7952 (tmt) cc_final: 0.7602 (tmm) REVERT: K 60 LYS cc_start: 0.7679 (tptt) cc_final: 0.6679 (ttpt) REVERT: K 176 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8396 (mm-40) REVERT: K 211 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8187 (t70) REVERT: K 215 ARG cc_start: 0.7424 (mpp80) cc_final: 0.6938 (mpp80) REVERT: K 304 LYS cc_start: 0.8560 (tppt) cc_final: 0.8057 (tppt) REVERT: K 370 LYS cc_start: 0.8160 (tttp) cc_final: 0.7739 (tppt) REVERT: K 377 MET cc_start: 0.7393 (ttp) cc_final: 0.7151 (ttp) REVERT: K 384 ILE cc_start: 0.8207 (pp) cc_final: 0.7477 (tt) REVERT: K 388 TRP cc_start: 0.7930 (m100) cc_final: 0.7531 (m100) REVERT: K 417 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8358 (tp30) REVERT: K 424 ASP cc_start: 0.8517 (t70) cc_final: 0.8297 (m-30) REVERT: K 425 MET cc_start: 0.8901 (mmm) cc_final: 0.8353 (tpp) REVERT: K 430 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8163 (mmtt) REVERT: C 259 ARG cc_start: 0.1046 (ttm170) cc_final: 0.0040 (tpp80) REVERT: E 148 MET cc_start: 0.3624 (mmm) cc_final: 0.2837 (mmm) REVERT: E 217 LEU cc_start: 0.4938 (pt) cc_final: 0.4118 (mp) outliers start: 58 outliers final: 38 residues processed: 361 average time/residue: 1.2396 time to fit residues: 508.7549 Evaluate side-chains 337 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 290 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 82 THR 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 269 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 156 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 363 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 30 ILE 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 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 267 MET Chi-restraints excluded: chain H residue 318 ARG Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 153 LEU Chi-restraints excluded: chain K residue 176 GLN Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain K residue 239 THR Chi-restraints excluded: chain K residue 257 THR 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 301 GLU Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 261 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.4314 > 50: distance: 20 - 146: 9.860 distance: 106 - 182: 16.412 distance: 109 - 179: 9.086 distance: 118 - 167: 23.374 distance: 121 - 164: 26.927 distance: 129 - 149: 29.125 distance: 132 - 146: 12.821 distance: 142 - 146: 10.531 distance: 146 - 147: 8.666 distance: 147 - 148: 10.422 distance: 147 - 150: 19.874 distance: 148 - 149: 15.197 distance: 148 - 157: 36.810 distance: 150 - 151: 18.637 distance: 151 - 152: 9.113 distance: 152 - 153: 16.010 distance: 153 - 154: 6.814 distance: 154 - 155: 10.571 distance: 154 - 156: 17.615 distance: 157 - 158: 13.458 distance: 157 - 163: 24.254 distance: 158 - 159: 23.783 distance: 159 - 160: 41.128 distance: 159 - 164: 10.710 distance: 161 - 162: 21.017 distance: 162 - 163: 13.857 distance: 164 - 165: 15.935 distance: 165 - 166: 15.391 distance: 165 - 168: 28.438 distance: 166 - 167: 30.377 distance: 166 - 171: 16.180 distance: 168 - 169: 16.080 distance: 168 - 170: 24.934 distance: 171 - 172: 14.397 distance: 172 - 173: 5.465 distance: 173 - 174: 8.941 distance: 173 - 179: 27.134 distance: 175 - 176: 21.053 distance: 176 - 177: 21.796 distance: 176 - 178: 19.335 distance: 179 - 180: 9.948 distance: 180 - 181: 16.921 distance: 180 - 183: 23.034 distance: 181 - 182: 21.296 distance: 181 - 184: 20.349 distance: 184 - 185: 11.887 distance: 185 - 186: 13.380 distance: 185 - 188: 18.298 distance: 186 - 187: 26.674 distance: 186 - 192: 43.175 distance: 188 - 189: 31.416 distance: 188 - 190: 34.319 distance: 189 - 191: 6.760 distance: 192 - 193: 14.320 distance: 193 - 194: 19.413 distance: 193 - 196: 25.238 distance: 194 - 195: 16.587 distance: 194 - 200: 18.752 distance: 196 - 197: 7.289 distance: 197 - 198: 23.148 distance: 197 - 199: 10.664 distance: 200 - 201: 18.074 distance: 201 - 202: 9.823 distance: 201 - 204: 17.255 distance: 202 - 203: 21.216 distance: 202 - 208: 27.053 distance: 204 - 205: 25.017 distance: 205 - 206: 41.740 distance: 205 - 207: 42.927 distance: 208 - 209: 10.636 distance: 209 - 210: 15.028 distance: 209 - 212: 23.513 distance: 210 - 211: 11.946 distance: 210 - 215: 41.406 distance: 212 - 213: 21.825 distance: 212 - 214: 11.095 distance: 215 - 216: 8.964 distance: 216 - 217: 9.983 distance: 217 - 219: 21.690