Starting phenix.real_space_refine on Sun Jan 19 05:04:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8utv_42551/01_2025/8utv_42551.cif Found real_map, /net/cci-nas-00/data/ceres_data/8utv_42551/01_2025/8utv_42551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8utv_42551/01_2025/8utv_42551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8utv_42551/01_2025/8utv_42551.map" model { file = "/net/cci-nas-00/data/ceres_data/8utv_42551/01_2025/8utv_42551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8utv_42551/01_2025/8utv_42551.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 2 5.21 5 S 87 5.16 5 C 8346 2.51 5 N 2277 2.21 5 O 2615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 13337 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3524 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 20, 'TRANS': 430} Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3411 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 413} Chain: "K" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2782 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 11, 'TRANS': 342} Chain: "E" 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: "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: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.29, per 1000 atoms: 0.62 Number of scatterers: 13337 At special positions: 0 Unit cell: (108.624, 78.84, 155.052, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 87 16.00 P 10 15.00 Mg 2 11.99 O 2615 8.00 N 2277 7.00 C 8346 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=0, symmetry=0 Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 2.0 seconds 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3114 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 14 sheets defined 48.7% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 37 through 43 Processing helix chain 'E' and resid 71 through 81 removed outlier: 4.466A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 86 removed outlier: 4.693A pdb=" N GLN E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 113 through 129 removed outlier: 3.867A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.209A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.581A pdb=" N ASN E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.769A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 277 through 282 removed outlier: 3.960A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.678A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 removed outlier: 3.510A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 3.961A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.976A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 436 Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.530A pdb=" N THR A 41 " --> pdb=" O PRO A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.652A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 4.642A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 113 through 129 removed outlier: 3.815A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.247A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.534A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.741A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.898A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.770A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 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 400 removed outlier: 3.955A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.027A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 436 Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.636A pdb=" N VAL B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.356A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.640A pdb=" N PHE B 85 " --> pdb=" O GLY B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.837A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.613A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.566A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 Processing helix chain 'B' and resid 249 through 258 removed outlier: 3.522A pdb=" N LEU B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 285 through 294 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 Processing helix chain 'B' and resid 338 through 341 removed outlier: 4.128A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.918A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.230A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.792A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 69 through 77 Processing helix chain 'K' and resid 77 through 87 Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 117 through 133 Processing helix chain 'K' and resid 188 through 201 Processing helix chain 'K' and resid 262 through 296 Proline residue: K 292 - end of helix Processing helix chain 'K' and resid 309 through 315 removed outlier: 3.653A pdb=" N TRP K 313 " --> pdb=" O SER K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 320 Processing helix chain 'K' and resid 337 through 350 removed outlier: 4.180A pdb=" N ARG K 350 " --> pdb=" O ARG K 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.291A pdb=" N GLU E 3 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLN E 133 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU E 167 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'E' and resid 269 through 272 Processing sheet with id=AA4, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.268A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 removed outlier: 8.341A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN B 165 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 267 through 271 Processing sheet with id=AB1, first strand: chain 'K' and resid 54 through 56 removed outlier: 3.524A pdb=" N LYS K 7 " --> pdb=" O THR K 325 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET K 327 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL K 91 " --> pdb=" O SER K 245 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL K 247 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE K 93 " --> pdb=" O VAL K 247 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 56 removed outlier: 3.524A pdb=" N LYS K 7 " --> pdb=" O THR K 325 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET K 327 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL K 91 " --> pdb=" O SER K 245 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL K 247 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE K 93 " --> pdb=" O VAL K 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 28 through 31 Processing sheet with id=AB4, first strand: chain 'K' and resid 168 through 171 Processing sheet with id=AB5, first strand: chain 'K' and resid 205 through 206 670 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.16 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2279 1.32 - 1.44: 3629 1.44 - 1.57: 7558 1.57 - 1.69: 21 1.69 - 1.82: 137 Bond restraints: 13624 Sorted by residual: bond pdb=" C ARG B 391 " pdb=" O ARG B 391 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.28e-02 6.10e+03 1.24e+01 bond pdb=" N ILE K 304 " pdb=" CA ILE K 304 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.15e-02 7.56e+03 8.85e+00 bond pdb=" N LEU A 217 " pdb=" CA LEU A 217 " ideal model delta sigma weight residual 1.455 1.492 -0.036 1.25e-02 6.40e+03 8.46e+00 bond pdb=" C PRO B 171 " pdb=" N SER B 172 " ideal model delta sigma weight residual 1.333 1.253 0.080 2.74e-02 1.33e+03 8.45e+00 bond pdb=" N GLU E 445 " pdb=" CA GLU E 445 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.23e-02 6.61e+03 8.25e+00 ... (remaining 13619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 17965 2.28 - 4.56: 439 4.56 - 6.84: 82 6.84 - 9.11: 8 9.11 - 11.39: 2 Bond angle restraints: 18496 Sorted by residual: angle pdb=" CA ARG B 391 " pdb=" C ARG B 391 " pdb=" O ARG B 391 " ideal model delta sigma weight residual 118.90 114.45 4.45 1.10e+00 8.26e-01 1.64e+01 angle pdb=" CA GLU E 445 " pdb=" C GLU E 445 " pdb=" N GLU E 446 " ideal model delta sigma weight residual 115.29 121.00 -5.71 1.42e+00 4.96e-01 1.61e+01 angle pdb=" C GLU E 445 " pdb=" N GLU E 446 " pdb=" CA GLU E 446 " ideal model delta sigma weight residual 123.09 115.43 7.66 1.94e+00 2.66e-01 1.56e+01 angle pdb=" CB MET K 138 " pdb=" CG MET K 138 " pdb=" SD MET K 138 " ideal model delta sigma weight residual 112.70 124.09 -11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb=" CA ASP A 218 " pdb=" C ASP A 218 " pdb=" O ASP A 218 " ideal model delta sigma weight residual 122.03 117.74 4.29 1.17e+00 7.31e-01 1.35e+01 ... (remaining 18491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.45: 7846 30.45 - 60.90: 320 60.90 - 91.35: 42 91.35 - 121.79: 4 121.79 - 152.24: 15 Dihedral angle restraints: 8227 sinusoidal: 3370 harmonic: 4857 Sorted by residual: 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 -138.49 -152.24 1 2.00e+01 2.50e-03 4.52e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -40.59 145.18 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -153.56 -137.17 1 2.00e+01 2.50e-03 4.16e+01 ... (remaining 8224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1573 0.053 - 0.105: 341 0.105 - 0.158: 105 0.158 - 0.210: 7 0.210 - 0.263: 3 Chirality restraints: 2029 Sorted by residual: chirality pdb=" CA ILE A 219 " pdb=" N ILE A 219 " pdb=" C ILE A 219 " pdb=" CB ILE A 219 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE K 282 " pdb=" CA ILE K 282 " pdb=" CG1 ILE K 282 " pdb=" CG2 ILE K 282 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB VAL K 73 " pdb=" CA VAL K 73 " pdb=" CG1 VAL K 73 " pdb=" CG2 VAL K 73 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 2026 not shown) Planarity restraints: 2402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY K 291 " 0.066 5.00e-02 4.00e+02 9.96e-02 1.59e+01 pdb=" N PRO K 292 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO K 292 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO K 292 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 435 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C VAL E 435 " -0.055 2.00e-02 2.50e+03 pdb=" O VAL E 435 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY E 436 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 24 " -0.017 2.00e-02 2.50e+03 2.09e-02 8.74e+00 pdb=" CG TYR A 24 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR A 24 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 24 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 24 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 24 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 24 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 24 " -0.001 2.00e-02 2.50e+03 ... (remaining 2399 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 204 2.65 - 3.21: 12558 3.21 - 3.78: 20067 3.78 - 4.34: 27757 4.34 - 4.90: 47211 Nonbonded interactions: 107797 Sorted by model distance: nonbonded pdb=" OH TYR K 74 " pdb=" OD2 ASP K 125 " model vdw 2.091 3.040 nonbonded pdb=" OG SER B 296 " pdb=" OD1 ASP B 304 " model vdw 2.095 3.040 nonbonded pdb=" OG SER E 178 " pdb=" OE1 GLU E 183 " model vdw 2.100 3.040 nonbonded pdb=" OG SER K 104 " pdb=" O2A ADP K 801 " model vdw 2.102 3.040 nonbonded pdb=" OG SER B 172 " pdb=" OE2 GLU B 205 " model vdw 2.148 3.040 ... (remaining 107792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 1 through 440 or resid 501 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 20.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 29.710 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.005 0.080 13624 Z= 0.337 Angle : 0.853 11.393 18496 Z= 0.465 Chirality : 0.049 0.263 2029 Planarity : 0.007 0.117 2402 Dihedral : 17.975 152.243 5113 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.07 % Favored : 95.87 % Rotamer: Outliers : 0.70 % Allowed : 13.24 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.10 (0.20), residues: 1671 helix: 1.01 (0.20), residues: 686 sheet: -0.01 (0.28), residues: 302 loop : -1.18 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 346 HIS 0.003 0.001 HIS A 88 PHE 0.021 0.002 PHE B 367 TYR 0.051 0.002 TYR A 24 ARG 0.017 0.001 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 303 time to evaluate : 1.410 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: E 49 PHE cc_start: 0.7313 (m-80) cc_final: 0.7110 (m-80) REVERT: E 190 THR cc_start: 0.8917 (p) cc_final: 0.8471 (t) REVERT: A 154 MET cc_start: 0.8333 (mmm) cc_final: 0.7950 (mmm) REVERT: A 190 THR cc_start: 0.8910 (p) cc_final: 0.8351 (t) REVERT: A 218 ASP cc_start: 0.8108 (t0) cc_final: 0.7877 (t0) REVERT: A 398 MET cc_start: 0.7921 (mtt) cc_final: 0.7719 (mtt) REVERT: B 14 ASN cc_start: 0.7896 (m-40) cc_final: 0.7623 (m-40) REVERT: K 149 ILE cc_start: 0.7993 (mm) cc_final: 0.7579 (mm) REVERT: K 337 ASN cc_start: 0.6689 (m110) cc_final: 0.5864 (t0) outliers start: 10 outliers final: 3 residues processed: 310 average time/residue: 1.3297 time to fit residues: 450.3844 Evaluate side-chains 247 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 244 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain K residue 132 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 50.0000 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 0.0770 chunk 97 optimal weight: 0.3980 chunk 151 optimal weight: 30.0000 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 358 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 204 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.148265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.103607 restraints weight = 19007.353| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.29 r_work: 0.3348 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13624 Z= 0.201 Angle : 0.650 10.152 18496 Z= 0.318 Chirality : 0.046 0.291 2029 Planarity : 0.005 0.091 2402 Dihedral : 13.307 157.451 1991 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.21 % Allowed : 14.22 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.30 (0.21), residues: 1671 helix: 1.33 (0.20), residues: 709 sheet: 0.34 (0.29), residues: 302 loop : -1.09 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 344 HIS 0.004 0.001 HIS K 84 PHE 0.018 0.001 PHE K 221 TYR 0.047 0.002 TYR A 24 ARG 0.006 0.001 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 282 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 PHE cc_start: 0.7813 (m-80) cc_final: 0.7607 (m-80) REVERT: E 76 ASP cc_start: 0.8399 (m-30) cc_final: 0.8182 (m-30) REVERT: E 128 GLN cc_start: 0.8537 (tm130) cc_final: 0.8320 (tt0) REVERT: E 279 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8483 (tp30) REVERT: E 313 MET cc_start: 0.8925 (mtm) cc_final: 0.8667 (mtp) REVERT: A 155 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8457 (mt-10) REVERT: A 214 ARG cc_start: 0.9199 (ttp-170) cc_final: 0.8858 (tmm-80) REVERT: A 218 ASP cc_start: 0.8887 (t0) cc_final: 0.8671 (t0) REVERT: A 420 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7825 (mt-10) REVERT: A 434 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8390 (tp30) REVERT: B 1 MET cc_start: 0.7170 (mpm) cc_final: 0.6810 (mmm) REVERT: B 86 ARG cc_start: 0.6440 (tpt170) cc_final: 0.4081 (ttp-110) REVERT: B 208 TYR cc_start: 0.8861 (m-10) cc_final: 0.8597 (m-10) REVERT: K 48 LYS cc_start: 0.8513 (mmtm) cc_final: 0.8154 (mppt) REVERT: K 56 TYR cc_start: 0.4440 (m-80) cc_final: 0.4101 (m-80) REVERT: K 63 GLU cc_start: 0.2231 (mt-10) cc_final: 0.1528 (tm-30) REVERT: K 147 MET cc_start: 0.6378 (tpt) cc_final: 0.5787 (tpt) REVERT: K 223 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7572 (pp) REVERT: K 264 ARG cc_start: 0.8140 (ttt180) cc_final: 0.7874 (tmt90) REVERT: K 265 LEU cc_start: 0.8066 (pp) cc_final: 0.7555 (pp) REVERT: K 306 TYR cc_start: 0.7031 (p90) cc_final: 0.6757 (p90) REVERT: K 335 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7056 (m-30) REVERT: K 337 ASN cc_start: 0.7080 (m110) cc_final: 0.6127 (t0) outliers start: 46 outliers final: 15 residues processed: 304 average time/residue: 1.1387 time to fit residues: 381.6297 Evaluate side-chains 258 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 239 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 335 ASP Chi-restraints excluded: chain K residue 336 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 52 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 chunk 151 optimal weight: 7.9990 chunk 136 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN A 356 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.147874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.102587 restraints weight = 19297.267| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.37 r_work: 0.3329 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13624 Z= 0.192 Angle : 0.624 15.133 18496 Z= 0.300 Chirality : 0.046 0.495 2029 Planarity : 0.004 0.084 2402 Dihedral : 11.064 156.899 1988 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.16 % Allowed : 16.52 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.48 (0.21), residues: 1671 helix: 1.51 (0.20), residues: 712 sheet: 0.53 (0.29), residues: 292 loop : -1.09 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 344 HIS 0.005 0.001 HIS A 192 PHE 0.017 0.001 PHE A 52 TYR 0.029 0.001 TYR A 24 ARG 0.006 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 259 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 PHE cc_start: 0.7827 (m-80) cc_final: 0.7614 (m-80) REVERT: E 77 GLU cc_start: 0.8569 (tt0) cc_final: 0.8324 (tt0) REVERT: E 207 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8227 (mt-10) REVERT: E 279 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8481 (tp30) REVERT: E 322 ASP cc_start: 0.8716 (t0) cc_final: 0.8499 (t0) REVERT: E 341 ILE cc_start: 0.9135 (mm) cc_final: 0.8871 (mp) REVERT: A 98 ASP cc_start: 0.7088 (t0) cc_final: 0.6844 (t0) REVERT: A 214 ARG cc_start: 0.9191 (ttp-170) cc_final: 0.8849 (tmm-80) REVERT: A 218 ASP cc_start: 0.8912 (t0) cc_final: 0.8680 (t0) REVERT: A 276 ILE cc_start: 0.8793 (tt) cc_final: 0.8491 (pp) REVERT: A 408 TYR cc_start: 0.8900 (m-80) cc_final: 0.8401 (m-80) REVERT: A 434 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8285 (tp30) REVERT: B 1 MET cc_start: 0.7283 (mpm) cc_final: 0.6868 (mmm) REVERT: B 86 ARG cc_start: 0.6263 (tpt170) cc_final: 0.3950 (ttp-170) REVERT: B 291 GLN cc_start: 0.8786 (pp30) cc_final: 0.8555 (pp30) REVERT: B 412 GLU cc_start: 0.7892 (tp30) cc_final: 0.7475 (tp30) REVERT: B 415 MET cc_start: 0.8327 (ttp) cc_final: 0.8088 (ttp) REVERT: B 423 GLN cc_start: 0.8523 (tp40) cc_final: 0.8314 (tp40) REVERT: K 63 GLU cc_start: 0.2329 (mt-10) cc_final: 0.1757 (tm-30) REVERT: K 126 LEU cc_start: 0.9163 (mt) cc_final: 0.8860 (pp) REVERT: K 147 MET cc_start: 0.5732 (tpt) cc_final: 0.5108 (tpt) REVERT: K 273 LYS cc_start: 0.8560 (tmmt) cc_final: 0.8246 (pptt) REVERT: K 335 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.6875 (m-30) REVERT: K 337 ASN cc_start: 0.7015 (m110) cc_final: 0.6126 (t0) outliers start: 31 outliers final: 15 residues processed: 272 average time/residue: 1.2423 time to fit residues: 370.6069 Evaluate side-chains 250 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 216 ARG Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 293 ASN Chi-restraints excluded: chain K residue 335 ASP Chi-restraints excluded: chain K residue 336 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 42 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 135 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 140 optimal weight: 30.0000 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.0980 chunk 56 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 ASN E 249 ASN ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN A 256 GLN A 356 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.148383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.103076 restraints weight = 19005.991| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.38 r_work: 0.3349 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13624 Z= 0.169 Angle : 0.596 10.604 18496 Z= 0.288 Chirality : 0.044 0.392 2029 Planarity : 0.004 0.081 2402 Dihedral : 10.249 155.663 1988 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.93 % Allowed : 17.77 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.57 (0.21), residues: 1671 helix: 1.64 (0.20), residues: 713 sheet: 0.45 (0.29), residues: 308 loop : -1.09 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.005 0.001 HIS A 192 PHE 0.013 0.001 PHE K 221 TYR 0.023 0.001 TYR A 24 ARG 0.009 0.000 ARG K 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 269 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.8596 (tt0) cc_final: 0.8370 (tt0) REVERT: E 128 GLN cc_start: 0.8590 (tm130) cc_final: 0.8296 (tt0) REVERT: E 207 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8235 (mt-10) REVERT: E 279 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8504 (tp30) REVERT: E 341 ILE cc_start: 0.9113 (mm) cc_final: 0.8846 (mp) REVERT: A 36 MET cc_start: 0.8028 (ttm) cc_final: 0.7820 (ttm) REVERT: A 218 ASP cc_start: 0.8889 (t0) cc_final: 0.8667 (t0) REVERT: A 276 ILE cc_start: 0.8812 (tt) cc_final: 0.8528 (pp) REVERT: A 420 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7854 (mt-10) REVERT: A 434 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8351 (tp30) REVERT: B 1 MET cc_start: 0.7376 (mpm) cc_final: 0.6948 (mmm) REVERT: B 86 ARG cc_start: 0.6250 (tpt170) cc_final: 0.4004 (ttm-80) REVERT: B 291 GLN cc_start: 0.8814 (pp30) cc_final: 0.8534 (pp30) REVERT: B 412 GLU cc_start: 0.7808 (tp30) cc_final: 0.7503 (tp30) REVERT: B 423 GLN cc_start: 0.8507 (tp40) cc_final: 0.8265 (tp40) REVERT: K 6 VAL cc_start: 0.7043 (t) cc_final: 0.6794 (p) REVERT: K 63 GLU cc_start: 0.2377 (mt-10) cc_final: 0.1853 (tm-30) REVERT: K 147 MET cc_start: 0.5441 (tpt) cc_final: 0.4939 (tpt) REVERT: K 181 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6214 (tm) REVERT: K 223 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7407 (pp) REVERT: K 246 LEU cc_start: 0.6216 (tm) cc_final: 0.5923 (pp) REVERT: K 273 LYS cc_start: 0.8585 (tmmt) cc_final: 0.8261 (pptt) REVERT: K 315 LEU cc_start: 0.8984 (mm) cc_final: 0.8303 (tm) REVERT: K 335 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.6899 (m-30) REVERT: K 337 ASN cc_start: 0.7107 (m110) cc_final: 0.6342 (t0) outliers start: 42 outliers final: 19 residues processed: 283 average time/residue: 1.1519 time to fit residues: 360.2427 Evaluate side-chains 256 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 285 GLN Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 293 ASN Chi-restraints excluded: chain K residue 335 ASP Chi-restraints excluded: chain K residue 336 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 165 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 148 optimal weight: 0.0470 chunk 99 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 249 ASN E 301 GLN A 101 ASN A 102 ASN A 192 HIS A 256 GLN A 356 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 414 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.146425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.101172 restraints weight = 19201.721| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.32 r_work: 0.3312 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13624 Z= 0.278 Angle : 0.650 17.356 18496 Z= 0.311 Chirality : 0.046 0.343 2029 Planarity : 0.004 0.077 2402 Dihedral : 10.082 150.938 1988 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.48 % Allowed : 18.40 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.52 (0.21), residues: 1671 helix: 1.64 (0.20), residues: 708 sheet: 0.38 (0.28), residues: 317 loop : -1.13 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 346 HIS 0.005 0.001 HIS A 192 PHE 0.014 0.002 PHE E 49 TYR 0.022 0.001 TYR A 24 ARG 0.008 0.000 ARG E 339 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 246 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 279 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8473 (tp30) REVERT: E 341 ILE cc_start: 0.9127 (mm) cc_final: 0.8852 (mp) REVERT: A 119 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8539 (mm) REVERT: A 168 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8405 (mm-30) REVERT: A 218 ASP cc_start: 0.8874 (t0) cc_final: 0.8371 (t0) REVERT: A 276 ILE cc_start: 0.8830 (tt) cc_final: 0.8558 (pp) REVERT: A 434 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8384 (tp30) REVERT: B 1 MET cc_start: 0.7611 (mpm) cc_final: 0.7210 (mmm) REVERT: B 73 MET cc_start: 0.8697 (mmm) cc_final: 0.8487 (mmm) REVERT: B 86 ARG cc_start: 0.6392 (tpt170) cc_final: 0.4034 (ttm-80) REVERT: B 205 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8396 (mp0) REVERT: B 230 SER cc_start: 0.9177 (m) cc_final: 0.8697 (p) REVERT: B 291 GLN cc_start: 0.8864 (pp30) cc_final: 0.8639 (pp30) REVERT: B 412 GLU cc_start: 0.7824 (tp30) cc_final: 0.7507 (tp30) REVERT: B 415 MET cc_start: 0.8318 (ttp) cc_final: 0.8112 (ttp) REVERT: B 423 GLN cc_start: 0.8530 (tp40) cc_final: 0.8271 (tp40) REVERT: K 63 GLU cc_start: 0.2426 (mt-10) cc_final: 0.1842 (tm-30) REVERT: K 147 MET cc_start: 0.5377 (tpt) cc_final: 0.4813 (tpt) REVERT: K 181 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6238 (tm) REVERT: K 196 MET cc_start: 0.7250 (ptt) cc_final: 0.7015 (pmm) REVERT: K 265 LEU cc_start: 0.8029 (pp) cc_final: 0.7707 (pp) REVERT: K 266 LYS cc_start: 0.8763 (mmtm) cc_final: 0.8534 (mmtm) REVERT: K 273 LYS cc_start: 0.8618 (tmmt) cc_final: 0.8315 (pptt) REVERT: K 335 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.6844 (m-30) REVERT: K 337 ASN cc_start: 0.7222 (m110) cc_final: 0.6418 (t0) REVERT: K 345 LEU cc_start: 0.8816 (tp) cc_final: 0.8609 (pp) outliers start: 50 outliers final: 25 residues processed: 268 average time/residue: 1.1568 time to fit residues: 342.6054 Evaluate side-chains 263 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 249 ASN Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 285 GLN Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 293 ASN Chi-restraints excluded: chain K residue 335 ASP Chi-restraints excluded: chain K residue 336 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 125 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 156 optimal weight: 50.0000 chunk 104 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 249 ASN A 356 ASN B 165 ASN B 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.145884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.101123 restraints weight = 19493.103| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.31 r_work: 0.3300 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13624 Z= 0.290 Angle : 0.639 13.880 18496 Z= 0.309 Chirality : 0.046 0.269 2029 Planarity : 0.004 0.077 2402 Dihedral : 10.214 145.331 1988 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.41 % Allowed : 18.61 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.49 (0.21), residues: 1671 helix: 1.62 (0.20), residues: 708 sheet: 0.36 (0.28), residues: 314 loop : -1.16 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 346 HIS 0.004 0.001 HIS E 88 PHE 0.016 0.002 PHE K 221 TYR 0.012 0.001 TYR K 150 ARG 0.009 0.000 ARG E 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 245 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 128 GLN cc_start: 0.8677 (tm130) cc_final: 0.8361 (tt0) REVERT: E 255 PHE cc_start: 0.8331 (t80) cc_final: 0.7979 (t80) REVERT: E 279 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8418 (tp30) REVERT: E 341 ILE cc_start: 0.9126 (mm) cc_final: 0.8856 (mp) REVERT: A 218 ASP cc_start: 0.8847 (t0) cc_final: 0.8384 (t0) REVERT: A 434 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8448 (tp30) REVERT: B 1 MET cc_start: 0.7839 (mpm) cc_final: 0.7430 (mmm) REVERT: B 73 MET cc_start: 0.8731 (mmm) cc_final: 0.8482 (mmm) REVERT: B 86 ARG cc_start: 0.6339 (tpt170) cc_final: 0.4001 (ttm-80) REVERT: B 230 SER cc_start: 0.9182 (m) cc_final: 0.8774 (p) REVERT: B 291 GLN cc_start: 0.8896 (pp30) cc_final: 0.8673 (pp30) REVERT: B 412 GLU cc_start: 0.7857 (tp30) cc_final: 0.7526 (tp30) REVERT: B 423 GLN cc_start: 0.8518 (tp40) cc_final: 0.8283 (tp40) REVERT: K 63 GLU cc_start: 0.2432 (mt-10) cc_final: 0.1821 (tm-30) REVERT: K 126 LEU cc_start: 0.9129 (mt) cc_final: 0.8804 (pp) REVERT: K 147 MET cc_start: 0.5492 (tpt) cc_final: 0.4740 (tpt) REVERT: K 181 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.6025 (tm) REVERT: K 196 MET cc_start: 0.7256 (ptt) cc_final: 0.7050 (pmm) REVERT: K 223 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7386 (pp) REVERT: K 265 LEU cc_start: 0.7940 (pp) cc_final: 0.7642 (pp) REVERT: K 273 LYS cc_start: 0.8670 (tmmt) cc_final: 0.8434 (pptt) REVERT: K 337 ASN cc_start: 0.7224 (m110) cc_final: 0.6420 (t0) outliers start: 49 outliers final: 26 residues processed: 263 average time/residue: 1.1966 time to fit residues: 345.8918 Evaluate side-chains 265 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 285 GLN Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 293 ASN Chi-restraints excluded: chain K residue 336 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 109 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 0.3980 chunk 138 optimal weight: 4.9990 chunk 117 optimal weight: 0.0170 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 0.0060 chunk 51 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 249 ASN E 256 GLN ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN A 356 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 347 ASN B 414 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.149540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.104051 restraints weight = 19076.622| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.36 r_work: 0.3370 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13624 Z= 0.151 Angle : 0.612 14.111 18496 Z= 0.291 Chirality : 0.044 0.253 2029 Planarity : 0.004 0.075 2402 Dihedral : 9.502 136.245 1988 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.44 % Allowed : 19.58 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.64 (0.21), residues: 1671 helix: 1.75 (0.20), residues: 709 sheet: 0.41 (0.28), residues: 312 loop : -1.06 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 344 HIS 0.002 0.000 HIS K 84 PHE 0.013 0.001 PHE K 94 TYR 0.013 0.001 TYR A 24 ARG 0.009 0.000 ARG E 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 255 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 128 GLN cc_start: 0.8580 (tm130) cc_final: 0.8264 (tt0) REVERT: E 207 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8177 (mt-10) REVERT: E 279 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8475 (tp30) REVERT: E 339 ARG cc_start: 0.8208 (tpp-160) cc_final: 0.7597 (mmp80) REVERT: E 341 ILE cc_start: 0.9064 (mm) cc_final: 0.8794 (mp) REVERT: A 31 GLN cc_start: 0.8480 (mt0) cc_final: 0.8236 (mt0) REVERT: A 199 ASP cc_start: 0.8895 (m-30) cc_final: 0.8588 (m-30) REVERT: A 214 ARG cc_start: 0.9194 (ttp-170) cc_final: 0.8880 (tmm-80) REVERT: A 218 ASP cc_start: 0.8782 (t0) cc_final: 0.8328 (t0) REVERT: A 339 ARG cc_start: 0.8255 (tpp-160) cc_final: 0.7875 (tmm160) REVERT: A 434 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8223 (tp30) REVERT: B 1 MET cc_start: 0.7804 (mpm) cc_final: 0.7380 (mmm) REVERT: B 86 ARG cc_start: 0.6210 (tpt170) cc_final: 0.3946 (ttm-80) REVERT: B 205 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8314 (mp0) REVERT: B 366 THR cc_start: 0.8551 (t) cc_final: 0.8105 (p) REVERT: B 412 GLU cc_start: 0.7799 (tp30) cc_final: 0.7520 (tp30) REVERT: B 423 GLN cc_start: 0.8436 (tp40) cc_final: 0.8152 (tp40) REVERT: K 63 GLU cc_start: 0.2573 (mt-10) cc_final: 0.1935 (tm-30) REVERT: K 147 MET cc_start: 0.5229 (tpt) cc_final: 0.4438 (tpt) REVERT: K 181 LEU cc_start: 0.6352 (tm) cc_final: 0.5919 (tm) REVERT: K 273 LYS cc_start: 0.8707 (tmmt) cc_final: 0.8493 (pptt) REVERT: K 335 ASP cc_start: 0.7762 (m-30) cc_final: 0.7028 (m-30) REVERT: K 337 ASN cc_start: 0.7120 (m110) cc_final: 0.6386 (t0) outliers start: 35 outliers final: 20 residues processed: 272 average time/residue: 1.1678 time to fit residues: 350.0069 Evaluate side-chains 258 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 293 ASN Chi-restraints excluded: chain K residue 336 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 147 optimal weight: 40.0000 chunk 126 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 165 optimal weight: 50.0000 chunk 119 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 102 ASN E 249 ASN E 256 GLN ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN A 356 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.148691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.103034 restraints weight = 19217.612| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.37 r_work: 0.3349 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13624 Z= 0.189 Angle : 0.634 17.262 18496 Z= 0.301 Chirality : 0.044 0.248 2029 Planarity : 0.004 0.076 2402 Dihedral : 9.733 132.369 1988 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.44 % Allowed : 20.56 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.68 (0.21), residues: 1671 helix: 1.80 (0.20), residues: 706 sheet: 0.40 (0.27), residues: 317 loop : -1.04 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 388 HIS 0.002 0.001 HIS K 84 PHE 0.017 0.001 PHE A 52 TYR 0.008 0.001 TYR K 105 ARG 0.015 0.000 ARG E 422 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 247 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 128 GLN cc_start: 0.8567 (tm130) cc_final: 0.8242 (tt0) REVERT: E 207 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8096 (mt-10) REVERT: E 279 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8486 (tp30) REVERT: E 341 ILE cc_start: 0.9058 (mm) cc_final: 0.8771 (mp) REVERT: E 384 ILE cc_start: 0.8320 (mp) cc_final: 0.8007 (mp) REVERT: A 31 GLN cc_start: 0.8476 (mt0) cc_final: 0.8256 (mt0) REVERT: A 214 ARG cc_start: 0.9177 (ttp-170) cc_final: 0.8854 (tmm-80) REVERT: A 218 ASP cc_start: 0.8748 (t0) cc_final: 0.8305 (t0) REVERT: A 276 ILE cc_start: 0.8854 (tt) cc_final: 0.8511 (pp) REVERT: A 339 ARG cc_start: 0.8201 (tpp-160) cc_final: 0.7898 (tmm160) REVERT: A 420 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7878 (mt-10) REVERT: A 434 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8251 (tp30) REVERT: B 1 MET cc_start: 0.7819 (mpm) cc_final: 0.7435 (mmm) REVERT: B 86 ARG cc_start: 0.6280 (tpt170) cc_final: 0.3971 (ttm-80) REVERT: B 412 GLU cc_start: 0.7827 (tp30) cc_final: 0.7530 (tp30) REVERT: B 423 GLN cc_start: 0.8492 (tp40) cc_final: 0.8201 (tp40) REVERT: K 63 GLU cc_start: 0.2570 (mt-10) cc_final: 0.1994 (tm-30) REVERT: K 147 MET cc_start: 0.5244 (tpt) cc_final: 0.4453 (tpt) REVERT: K 155 ARG cc_start: 0.7951 (mtm180) cc_final: 0.7427 (mtm-85) REVERT: K 181 LEU cc_start: 0.6697 (tm) cc_final: 0.6357 (tm) REVERT: K 273 LYS cc_start: 0.8734 (tmmt) cc_final: 0.8519 (pptt) REVERT: K 335 ASP cc_start: 0.7884 (m-30) cc_final: 0.7637 (m-30) REVERT: K 337 ASN cc_start: 0.7188 (m110) cc_final: 0.6388 (t0) outliers start: 35 outliers final: 27 residues processed: 263 average time/residue: 1.1876 time to fit residues: 343.2167 Evaluate side-chains 263 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 235 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 293 ASN Chi-restraints excluded: chain K residue 336 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 52.2489 > 50: distance: 82 - 100: 14.303 distance: 86 - 106: 7.408 distance: 90 - 115: 7.094 distance: 95 - 100: 14.505 distance: 96 - 127: 6.408 distance: 100 - 101: 21.516 distance: 101 - 102: 28.859 distance: 101 - 104: 19.768 distance: 102 - 103: 23.749 distance: 102 - 106: 25.601 distance: 103 - 136: 8.799 distance: 104 - 105: 8.183 distance: 106 - 107: 14.442 distance: 107 - 108: 9.563 distance: 107 - 110: 11.714 distance: 108 - 109: 7.032 distance: 108 - 115: 12.762 distance: 111 - 112: 6.621 distance: 112 - 113: 6.295 distance: 112 - 114: 7.316 distance: 115 - 116: 8.324 distance: 116 - 117: 12.888 distance: 116 - 119: 7.740 distance: 117 - 118: 10.318 distance: 117 - 127: 12.076 distance: 119 - 120: 3.575 distance: 120 - 121: 8.097 distance: 121 - 123: 4.893 distance: 122 - 124: 3.821 distance: 123 - 125: 5.251 distance: 124 - 125: 4.680 distance: 127 - 128: 7.026 distance: 128 - 129: 11.153 distance: 128 - 131: 5.128 distance: 129 - 130: 13.117 distance: 129 - 136: 9.648 distance: 131 - 132: 4.235 distance: 132 - 133: 8.526 distance: 133 - 134: 6.476 distance: 133 - 135: 11.565 distance: 136 - 137: 11.090 distance: 137 - 138: 6.061 distance: 137 - 140: 7.948 distance: 138 - 139: 6.426 distance: 138 - 145: 8.593 distance: 141 - 142: 5.496 distance: 142 - 143: 5.698 distance: 142 - 144: 8.943 distance: 145 - 146: 12.103 distance: 146 - 147: 12.848 distance: 147 - 148: 6.207 distance: 147 - 157: 30.258 distance: 149 - 150: 8.132 distance: 150 - 151: 7.784 distance: 151 - 153: 9.827 distance: 152 - 154: 6.645 distance: 153 - 155: 5.906 distance: 154 - 155: 8.407 distance: 155 - 156: 5.763 distance: 157 - 158: 26.347 distance: 158 - 159: 33.784 distance: 158 - 161: 9.932 distance: 159 - 160: 47.850 distance: 159 - 166: 22.247 distance: 161 - 162: 19.232 distance: 162 - 163: 9.281 distance: 163 - 165: 21.446 distance: 166 - 167: 15.653 distance: 167 - 168: 21.377 distance: 167 - 170: 36.897 distance: 168 - 169: 33.582 distance: 168 - 174: 17.460 distance: 170 - 171: 25.134 distance: 171 - 172: 18.070 distance: 171 - 173: 30.181 distance: 174 - 175: 10.745 distance: 175 - 176: 13.205 distance: 175 - 178: 19.892 distance: 176 - 177: 9.041 distance: 176 - 179: 10.668 distance: 179 - 180: 11.946 distance: 180 - 181: 11.182 distance: 180 - 183: 15.111 distance: 181 - 182: 16.028 distance: 181 - 186: 6.868 distance: 183 - 184: 16.465 distance: 183 - 185: 5.322