Starting phenix.real_space_refine on Sat Aug 23 16:30:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8utv_42551/08_2025/8utv_42551.cif Found real_map, /net/cci-nas-00/data/ceres_data/8utv_42551/08_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_42551/08_2025/8utv_42551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8utv_42551/08_2025/8utv_42551.map" model { file = "/net/cci-nas-00/data/ceres_data/8utv_42551/08_2025/8utv_42551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8utv_42551/08_2025/8utv_42551.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.75, per 1000 atoms: 0.28 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: 1.24 Conformation dependent library (CDL) restraints added in 631.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.50 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: 2.35 Time building geometry restraints manager: 1.58 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: 4.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.580 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- 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= 0.256 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.017 0.001 ARG B 320 TYR 0.051 0.002 TYR A 24 PHE 0.021 0.002 PHE B 367 TRP 0.017 0.002 TRP E 346 HIS 0.003 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00511 (13624) covalent geometry : angle 0.85338 (18496) hydrogen bonds : bond 0.16009 ( 636) hydrogen bonds : angle 6.19591 ( 1908) *********************** 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 : 0.560 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: 0.6445 time to fit residues: 217.5017 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 : 0.634 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0570 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 204 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.146405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.101627 restraints weight = 18899.863| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.27 r_work: 0.3317 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13624 Z= 0.170 Angle : 0.671 10.157 18496 Z= 0.329 Chirality : 0.047 0.270 2029 Planarity : 0.005 0.091 2402 Dihedral : 13.560 156.640 1991 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.34 % Allowed : 14.43 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.21), residues: 1671 helix: 1.29 (0.20), residues: 707 sheet: 0.33 (0.29), residues: 302 loop : -1.15 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 215 TYR 0.046 0.002 TYR A 24 PHE 0.018 0.002 PHE K 221 TRP 0.020 0.002 TRP B 344 HIS 0.005 0.001 HIS K 84 Details of bonding type rmsd covalent geometry : bond 0.00391 (13624) covalent geometry : angle 0.67078 (18496) hydrogen bonds : bond 0.05063 ( 636) hydrogen bonds : angle 4.58714 ( 1908) *********************** 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 320 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 ASP cc_start: 0.8418 (m-30) cc_final: 0.8202 (m-30) REVERT: E 128 GLN cc_start: 0.8579 (tm130) cc_final: 0.8365 (tt0) REVERT: E 313 MET cc_start: 0.8981 (mtm) cc_final: 0.8731 (mtp) REVERT: A 155 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8453 (mt-10) REVERT: A 214 ARG cc_start: 0.9220 (ttp-170) cc_final: 0.8879 (tmm-80) REVERT: A 218 ASP cc_start: 0.8865 (t0) cc_final: 0.8645 (t0) REVERT: A 420 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7879 (mt-10) REVERT: A 434 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8379 (tp30) REVERT: B 1 MET cc_start: 0.7187 (mpm) cc_final: 0.6810 (mmm) REVERT: B 86 ARG cc_start: 0.6288 (tpt170) cc_final: 0.4012 (ttp-110) REVERT: B 208 TYR cc_start: 0.8868 (m-10) cc_final: 0.8566 (m-10) REVERT: K 48 LYS cc_start: 0.8540 (mmtm) cc_final: 0.8182 (mppt) REVERT: K 56 TYR cc_start: 0.4451 (m-80) cc_final: 0.4080 (m-80) REVERT: K 63 GLU cc_start: 0.2317 (mt-10) cc_final: 0.1523 (tm-30) REVERT: K 147 MET cc_start: 0.6394 (tpt) cc_final: 0.5756 (tpt) REVERT: K 223 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7632 (pp) REVERT: K 264 ARG cc_start: 0.8191 (ttt180) cc_final: 0.7952 (tmt90) REVERT: K 306 TYR cc_start: 0.7080 (p90) cc_final: 0.6815 (p90) REVERT: K 337 ASN cc_start: 0.7057 (OUTLIER) cc_final: 0.6088 (t0) outliers start: 48 outliers final: 19 residues processed: 294 average time/residue: 0.5842 time to fit residues: 189.3610 Evaluate side-chains 268 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 246 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 337 THR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 155 GLU 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 366 THR Chi-restraints excluded: chain B residue 404 ASP 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 336 ILE Chi-restraints excluded: chain K residue 337 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 68 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 134 optimal weight: 50.0000 chunk 71 optimal weight: 3.9990 chunk 156 optimal weight: 40.0000 chunk 34 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4190 r_free = 0.4190 target = 0.144573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.100309 restraints weight = 19305.506| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.27 r_work: 0.3278 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13624 Z= 0.206 Angle : 0.665 15.266 18496 Z= 0.324 Chirality : 0.048 0.488 2029 Planarity : 0.005 0.085 2402 Dihedral : 11.699 153.619 1988 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.34 % Allowed : 16.17 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.20), residues: 1671 helix: 1.38 (0.20), residues: 710 sheet: 0.42 (0.29), residues: 293 loop : -1.24 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 422 TYR 0.030 0.002 TYR A 24 PHE 0.015 0.002 PHE E 255 TRP 0.013 0.002 TRP B 344 HIS 0.005 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00482 (13624) covalent geometry : angle 0.66453 (18496) hydrogen bonds : bond 0.04901 ( 636) hydrogen bonds : angle 4.41933 ( 1908) *********************** 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 301 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 253 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.8576 (tt0) cc_final: 0.8318 (tt0) REVERT: E 279 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8349 (tp30) REVERT: E 341 ILE cc_start: 0.9156 (mm) cc_final: 0.8893 (mp) REVERT: A 98 ASP cc_start: 0.7187 (t0) cc_final: 0.6887 (t0) REVERT: A 155 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8517 (mt-10) REVERT: A 214 ARG cc_start: 0.9215 (ttp-170) cc_final: 0.8880 (tmm-80) REVERT: A 218 ASP cc_start: 0.8925 (t0) cc_final: 0.8690 (t0) REVERT: A 313 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8918 (mtp) REVERT: A 420 GLU cc_start: 0.8247 (mt-10) cc_final: 0.8029 (mt-10) REVERT: A 434 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8351 (tp30) REVERT: B 1 MET cc_start: 0.7610 (mpm) cc_final: 0.7230 (mmm) REVERT: B 86 ARG cc_start: 0.6323 (tpt170) cc_final: 0.4041 (ttm-80) REVERT: B 162 ARG cc_start: 0.8871 (mpt90) cc_final: 0.8374 (mmp-170) REVERT: B 217 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8973 (mp) REVERT: B 230 SER cc_start: 0.9182 (m) cc_final: 0.8748 (p) REVERT: B 291 GLN cc_start: 0.8812 (pp30) cc_final: 0.8594 (pp30) REVERT: B 415 MET cc_start: 0.8391 (ttp) cc_final: 0.8137 (ttp) REVERT: K 63 GLU cc_start: 0.2325 (mt-10) cc_final: 0.1744 (tm-30) REVERT: K 147 MET cc_start: 0.5712 (tpt) cc_final: 0.5096 (tpt) REVERT: K 223 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7430 (pp) REVERT: K 264 ARG cc_start: 0.8082 (ttt180) cc_final: 0.7830 (tmt90) REVERT: K 265 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7633 (pp) REVERT: K 273 LYS cc_start: 0.8573 (tmmt) cc_final: 0.8264 (pptt) REVERT: K 337 ASN cc_start: 0.7027 (m110) cc_final: 0.6094 (t0) outliers start: 48 outliers final: 26 residues processed: 274 average time/residue: 0.6199 time to fit residues: 185.3221 Evaluate side-chains 266 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 159 VAL 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 259 LEU 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 155 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 313 MET 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 209 ASP Chi-restraints excluded: chain B residue 217 LEU 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 223 ILE Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 293 ASN Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain K residue 345 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 79 optimal weight: 0.0040 chunk 50 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 27 optimal weight: 0.0870 chunk 5 optimal weight: 4.9990 chunk 159 optimal weight: 8.9990 chunk 163 optimal weight: 30.0000 chunk 126 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 overall best weight: 0.4370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 256 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.146922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.102249 restraints weight = 19129.592| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.29 r_work: 0.3333 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13624 Z= 0.116 Angle : 0.616 12.362 18496 Z= 0.295 Chirality : 0.044 0.425 2029 Planarity : 0.004 0.081 2402 Dihedral : 10.798 154.883 1988 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.51 % Allowed : 17.77 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.21), residues: 1671 helix: 1.59 (0.20), residues: 712 sheet: 0.33 (0.29), residues: 310 loop : -1.18 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 339 TYR 0.025 0.001 TYR A 24 PHE 0.013 0.001 PHE K 221 TRP 0.014 0.001 TRP B 344 HIS 0.005 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00249 (13624) covalent geometry : angle 0.61555 (18496) hydrogen bonds : bond 0.03955 ( 636) hydrogen bonds : angle 4.17204 ( 1908) *********************** 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 293 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 257 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.8582 (tt0) cc_final: 0.8360 (tt0) REVERT: E 128 GLN cc_start: 0.8597 (tm130) cc_final: 0.8332 (tt0) REVERT: E 322 ASP cc_start: 0.8702 (t0) cc_final: 0.8476 (t0) REVERT: E 339 ARG cc_start: 0.8126 (tpp-160) cc_final: 0.7552 (mmp80) REVERT: E 341 ILE cc_start: 0.9121 (mm) cc_final: 0.8860 (mp) REVERT: A 98 ASP cc_start: 0.7070 (t0) cc_final: 0.6864 (t0) REVERT: A 155 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8461 (mt-10) REVERT: A 214 ARG cc_start: 0.9176 (ttp-170) cc_final: 0.8859 (tmm-80) REVERT: A 218 ASP cc_start: 0.8868 (t0) cc_final: 0.8399 (t0) REVERT: A 276 ILE cc_start: 0.8781 (tt) cc_final: 0.8519 (pp) REVERT: A 341 ILE cc_start: 0.9186 (mm) cc_final: 0.8913 (mp) REVERT: A 420 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7851 (mt-10) REVERT: A 434 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8351 (tp30) REVERT: B 1 MET cc_start: 0.7574 (mpm) cc_final: 0.7195 (mmm) REVERT: B 86 ARG cc_start: 0.6299 (tpt170) cc_final: 0.4101 (ttm-80) REVERT: B 205 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: B 291 GLN cc_start: 0.8823 (pp30) cc_final: 0.8554 (pp30) REVERT: B 412 GLU cc_start: 0.7858 (tp30) cc_final: 0.7458 (tp30) REVERT: B 415 MET cc_start: 0.8315 (ttp) cc_final: 0.8064 (ttp) REVERT: B 423 GLN cc_start: 0.8499 (tp40) cc_final: 0.8263 (tp40) REVERT: K 63 GLU cc_start: 0.2449 (mt-10) cc_final: 0.1827 (tm-30) REVERT: K 126 LEU cc_start: 0.9096 (mt) cc_final: 0.8762 (pp) REVERT: K 147 MET cc_start: 0.5595 (tpt) cc_final: 0.5059 (tpt) REVERT: K 181 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6255 (tm) REVERT: K 273 LYS cc_start: 0.8579 (tmmt) cc_final: 0.8275 (pptt) REVERT: K 335 ASP cc_start: 0.8022 (m-30) cc_final: 0.7103 (m-30) REVERT: K 337 ASN cc_start: 0.7080 (m110) cc_final: 0.6273 (t0) outliers start: 36 outliers final: 16 residues processed: 272 average time/residue: 0.5976 time to fit residues: 178.1538 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 : 0.584 ------------------------------------------------------------------------------- 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 295 CYS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 155 GLU 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 205 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 44 optimal weight: 30.0000 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.145544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.101460 restraints weight = 19288.829| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.28 r_work: 0.3300 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2527 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= 0.169 Angle : 0.623 8.872 18496 Z= 0.302 Chirality : 0.045 0.316 2029 Planarity : 0.004 0.078 2402 Dihedral : 10.601 151.609 1988 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.28 % Allowed : 18.33 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.21), residues: 1671 helix: 1.70 (0.20), residues: 707 sheet: 0.30 (0.28), residues: 317 loop : -1.16 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 155 TYR 0.025 0.001 TYR A 24 PHE 0.014 0.002 PHE E 49 TRP 0.010 0.001 TRP E 346 HIS 0.005 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00395 (13624) covalent geometry : angle 0.62276 (18496) hydrogen bonds : bond 0.04290 ( 636) hydrogen bonds : angle 4.16621 ( 1908) *********************** 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 287 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 240 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.8617 (tt0) cc_final: 0.8396 (tt0) REVERT: E 341 ILE cc_start: 0.9131 (mm) cc_final: 0.8855 (mp) REVERT: A 155 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8484 (mt-10) REVERT: A 214 ARG cc_start: 0.9168 (ttp-170) cc_final: 0.8844 (tmm-80) REVERT: A 218 ASP cc_start: 0.8885 (t0) cc_final: 0.8408 (t0) REVERT: A 234 ILE cc_start: 0.8884 (mt) cc_final: 0.8679 (mt) REVERT: A 276 ILE cc_start: 0.8828 (tt) cc_final: 0.8544 (pp) REVERT: A 434 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8420 (tp30) REVERT: B 1 MET cc_start: 0.7755 (mpm) cc_final: 0.7359 (mmm) REVERT: B 86 ARG cc_start: 0.6357 (tpt170) cc_final: 0.4073 (ttm-80) REVERT: B 179 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8962 (t) REVERT: B 205 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8377 (mp0) REVERT: B 230 SER cc_start: 0.9166 (m) cc_final: 0.8741 (p) REVERT: B 291 GLN cc_start: 0.8886 (pp30) cc_final: 0.8671 (pp30) REVERT: B 320 ARG cc_start: 0.8525 (mmm-85) cc_final: 0.8269 (mmm-85) REVERT: B 412 GLU cc_start: 0.7853 (tp30) cc_final: 0.7557 (tp30) REVERT: B 415 MET cc_start: 0.8332 (ttp) cc_final: 0.8090 (ttp) REVERT: B 423 GLN cc_start: 0.8539 (tp40) cc_final: 0.8277 (tp40) REVERT: K 63 GLU cc_start: 0.2560 (mt-10) cc_final: 0.1844 (tm-30) REVERT: K 93 ILE cc_start: 0.7296 (mt) cc_final: 0.7039 (mt) REVERT: K 147 MET cc_start: 0.5337 (tpt) cc_final: 0.4756 (tpt) REVERT: K 181 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6197 (tm) REVERT: K 223 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7448 (pp) REVERT: K 273 LYS cc_start: 0.8650 (tmmt) cc_final: 0.8351 (pptt) REVERT: K 337 ASN cc_start: 0.7059 (m110) cc_final: 0.6198 (t0) outliers start: 47 outliers final: 24 residues processed: 259 average time/residue: 0.5841 time to fit residues: 166.6435 Evaluate side-chains 267 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 238 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 55 GLU 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 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 155 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 138 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 205 GLU 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 132 ASP Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 223 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 73 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 0.0570 chunk 52 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN E 256 GLN ** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.147033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.102337 restraints weight = 19170.955| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.35 r_work: 0.3345 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13624 Z= 0.115 Angle : 0.606 13.793 18496 Z= 0.291 Chirality : 0.044 0.307 2029 Planarity : 0.004 0.077 2402 Dihedral : 9.817 146.074 1988 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.72 % Allowed : 18.75 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.21), residues: 1671 helix: 1.73 (0.20), residues: 708 sheet: 0.31 (0.28), residues: 318 loop : -1.08 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 339 TYR 0.023 0.001 TYR A 24 PHE 0.018 0.001 PHE K 221 TRP 0.021 0.002 TRP B 344 HIS 0.003 0.000 HIS K 84 Details of bonding type rmsd covalent geometry : bond 0.00258 (13624) covalent geometry : angle 0.60591 (18496) hydrogen bonds : bond 0.03663 ( 636) hydrogen bonds : angle 4.01477 ( 1908) *********************** 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 296 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 257 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.8613 (tt0) cc_final: 0.8400 (tt0) REVERT: E 128 GLN cc_start: 0.8607 (tm130) cc_final: 0.8310 (tt0) REVERT: E 322 ASP cc_start: 0.8668 (t0) cc_final: 0.8465 (t0) REVERT: E 341 ILE cc_start: 0.9085 (mm) cc_final: 0.8801 (mp) REVERT: A 214 ARG cc_start: 0.9153 (ttp-170) cc_final: 0.8828 (tmm-80) REVERT: A 218 ASP cc_start: 0.8881 (t0) cc_final: 0.8502 (t0) REVERT: A 276 ILE cc_start: 0.8776 (tt) cc_final: 0.8544 (pp) REVERT: A 339 ARG cc_start: 0.8322 (tpp-160) cc_final: 0.7958 (tmm160) REVERT: A 341 ILE cc_start: 0.9166 (mm) cc_final: 0.8861 (mp) REVERT: A 345 ASP cc_start: 0.8465 (p0) cc_final: 0.8223 (p0) REVERT: A 408 TYR cc_start: 0.8822 (m-80) cc_final: 0.8572 (m-80) REVERT: A 434 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8409 (tp30) REVERT: B 1 MET cc_start: 0.7737 (mpm) cc_final: 0.7330 (mmm) REVERT: B 86 ARG cc_start: 0.6300 (tpt170) cc_final: 0.4005 (ttm-80) REVERT: B 230 SER cc_start: 0.9141 (m) cc_final: 0.8752 (p) REVERT: B 291 GLN cc_start: 0.8898 (pp30) cc_final: 0.8683 (pp30) REVERT: B 320 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.8375 (mmm-85) REVERT: B 412 GLU cc_start: 0.7804 (tp30) cc_final: 0.7558 (tp30) REVERT: B 423 GLN cc_start: 0.8492 (tp40) cc_final: 0.8230 (tp40) REVERT: K 147 MET cc_start: 0.5444 (tpt) cc_final: 0.4713 (tpt) REVERT: K 181 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.5995 (tm) REVERT: K 265 LEU cc_start: 0.7998 (pp) cc_final: 0.7764 (pp) REVERT: K 266 LYS cc_start: 0.8614 (mmtp) cc_final: 0.8336 (mmtt) REVERT: K 273 LYS cc_start: 0.8677 (tmmt) cc_final: 0.8378 (pptt) REVERT: K 337 ASN cc_start: 0.7246 (m110) cc_final: 0.6451 (t0) outliers start: 39 outliers final: 14 residues processed: 275 average time/residue: 0.5845 time to fit residues: 176.8322 Evaluate side-chains 255 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 240 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 241 SER Chi-restraints excluded: chain E residue 295 CYS 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 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 366 THR 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 293 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 67 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 162 optimal weight: 20.0000 chunk 135 optimal weight: 30.0000 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 153 optimal weight: 40.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 176 GLN A 256 GLN A 356 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN K 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.145244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.100756 restraints weight = 19311.475| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.29 r_work: 0.3300 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13624 Z= 0.187 Angle : 0.657 12.863 18496 Z= 0.318 Chirality : 0.046 0.272 2029 Planarity : 0.004 0.077 2402 Dihedral : 9.846 138.151 1988 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.07 % Allowed : 18.75 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.21), residues: 1671 helix: 1.65 (0.20), residues: 708 sheet: 0.28 (0.28), residues: 317 loop : -1.11 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 339 TYR 0.012 0.001 TYR K 150 PHE 0.015 0.002 PHE E 49 TRP 0.011 0.001 TRP A 388 HIS 0.005 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00446 (13624) covalent geometry : angle 0.65696 (18496) hydrogen bonds : bond 0.04285 ( 636) hydrogen bonds : angle 4.10979 ( 1908) *********************** 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 288 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 244 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.8610 (tt0) cc_final: 0.8392 (tt0) REVERT: E 128 GLN cc_start: 0.8649 (tm130) cc_final: 0.8400 (OUTLIER) REVERT: E 255 PHE cc_start: 0.8300 (t80) cc_final: 0.7834 (t80) REVERT: E 341 ILE cc_start: 0.9118 (mm) cc_final: 0.8840 (mp) REVERT: E 377 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7653 (tpp) REVERT: E 384 ILE cc_start: 0.8446 (mp) cc_final: 0.8137 (mp) REVERT: A 218 ASP cc_start: 0.8893 (t0) cc_final: 0.8482 (t0) REVERT: A 276 ILE cc_start: 0.8821 (tt) cc_final: 0.8585 (pp) REVERT: A 434 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8395 (tp30) REVERT: B 1 MET cc_start: 0.7891 (mpm) cc_final: 0.7497 (mmm) REVERT: B 86 ARG cc_start: 0.6283 (tpt170) cc_final: 0.3992 (ttm-80) REVERT: B 230 SER cc_start: 0.9174 (m) cc_final: 0.8840 (p) REVERT: B 291 GLN cc_start: 0.8907 (pp30) cc_final: 0.8701 (pp30) REVERT: B 320 ARG cc_start: 0.8590 (mmm-85) cc_final: 0.8369 (mmm-85) REVERT: B 412 GLU cc_start: 0.7863 (tp30) cc_final: 0.7522 (tp30) REVERT: B 423 GLN cc_start: 0.8522 (tp40) cc_final: 0.8228 (tp40) REVERT: K 63 GLU cc_start: 0.2488 (mt-10) cc_final: 0.1751 (tm-30) REVERT: K 147 MET cc_start: 0.5414 (tpt) cc_final: 0.4711 (tpt) REVERT: K 181 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.5878 (tm) REVERT: K 223 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7324 (pp) REVERT: K 273 LYS cc_start: 0.8704 (tmmt) cc_final: 0.8424 (pptt) REVERT: K 337 ASN cc_start: 0.7152 (m110) cc_final: 0.6346 (t0) outliers start: 44 outliers final: 27 residues processed: 264 average time/residue: 0.5697 time to fit residues: 166.3989 Evaluate side-chains 263 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 295 CYS Chi-restraints excluded: chain E residue 377 MET 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 248 LEU 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 138 SER Chi-restraints excluded: chain B residue 209 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 424 GLN Chi-restraints excluded: chain B residue 429 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 122 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 97 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 161 optimal weight: 20.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 176 GLN E 256 GLN ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.147297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.102418 restraints weight = 18969.064| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.29 r_work: 0.3341 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13624 Z= 0.120 Angle : 0.625 12.877 18496 Z= 0.300 Chirality : 0.044 0.253 2029 Planarity : 0.004 0.077 2402 Dihedral : 9.570 135.353 1986 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.30 % Allowed : 20.49 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.21), residues: 1671 helix: 1.73 (0.20), residues: 708 sheet: 0.30 (0.27), residues: 317 loop : -1.07 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 339 TYR 0.009 0.001 TYR E 24 PHE 0.012 0.001 PHE K 221 TRP 0.019 0.002 TRP A 388 HIS 0.002 0.000 HIS K 84 Details of bonding type rmsd covalent geometry : bond 0.00271 (13624) covalent geometry : angle 0.62516 (18496) hydrogen bonds : bond 0.03723 ( 636) hydrogen bonds : angle 4.00606 ( 1908) *********************** 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 286 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 253 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.8614 (tt0) cc_final: 0.8378 (tt0) REVERT: E 128 GLN cc_start: 0.8586 (tm130) cc_final: 0.8284 (tt0) REVERT: E 322 ASP cc_start: 0.8659 (t0) cc_final: 0.8456 (t0) REVERT: E 341 ILE cc_start: 0.9078 (mm) cc_final: 0.8791 (mp) REVERT: A 214 ARG cc_start: 0.9184 (ttp-170) cc_final: 0.8860 (tmm-80) REVERT: A 218 ASP cc_start: 0.8798 (t0) cc_final: 0.8384 (t0) REVERT: A 339 ARG cc_start: 0.8342 (tpp-160) cc_final: 0.7974 (tmm160) REVERT: A 392 ASP cc_start: 0.8585 (t0) cc_final: 0.8333 (t70) REVERT: A 422 ARG cc_start: 0.7933 (mmm160) cc_final: 0.7707 (mmm160) REVERT: A 434 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8356 (tp30) REVERT: B 1 MET cc_start: 0.7892 (mpm) cc_final: 0.7491 (mmm) REVERT: B 86 ARG cc_start: 0.6306 (OUTLIER) cc_final: 0.4005 (ttm-80) REVERT: B 205 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8242 (mp0) REVERT: B 320 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.8360 (mmm-85) REVERT: B 412 GLU cc_start: 0.7806 (tp30) cc_final: 0.7532 (tp30) REVERT: B 423 GLN cc_start: 0.8507 (tp40) cc_final: 0.8206 (tp40) REVERT: K 63 GLU cc_start: 0.2651 (mt-10) cc_final: 0.1895 (tm-30) REVERT: K 147 MET cc_start: 0.5151 (tpt) cc_final: 0.4388 (tpt) REVERT: K 181 LEU cc_start: 0.6608 (tm) cc_final: 0.6228 (tm) REVERT: K 265 LEU cc_start: 0.7973 (pp) cc_final: 0.7583 (pp) REVERT: K 266 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8489 (mmtm) REVERT: K 273 LYS cc_start: 0.8718 (tmmt) cc_final: 0.8442 (pptt) outliers start: 33 outliers final: 22 residues processed: 266 average time/residue: 0.5920 time to fit residues: 172.9983 Evaluate side-chains 265 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 242 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 241 SER 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 295 CYS Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 322 SER 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 132 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 0.0050 chunk 70 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 142 optimal weight: 30.0000 chunk 85 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN 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 347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.148977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.103543 restraints weight = 19309.178| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.40 r_work: 0.3363 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3147 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= 0.113 Angle : 0.641 13.118 18496 Z= 0.308 Chirality : 0.044 0.292 2029 Planarity : 0.004 0.076 2402 Dihedral : 9.377 132.632 1986 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.44 % Allowed : 20.98 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.21), residues: 1671 helix: 1.79 (0.20), residues: 707 sheet: 0.34 (0.27), residues: 317 loop : -1.05 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 339 TYR 0.010 0.001 TYR E 24 PHE 0.016 0.001 PHE B 212 TRP 0.024 0.002 TRP B 344 HIS 0.002 0.000 HIS K 84 Details of bonding type rmsd covalent geometry : bond 0.00250 (13624) covalent geometry : angle 0.64147 (18496) hydrogen bonds : bond 0.03555 ( 636) hydrogen bonds : angle 4.03560 ( 1908) *********************** REFINEMENT MACRO_CYCLE 9 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 287 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.8607 (tt0) cc_final: 0.8392 (tt0) REVERT: E 128 GLN cc_start: 0.8545 (tm130) cc_final: 0.8269 (tt0) REVERT: E 279 GLU cc_start: 0.8656 (tp30) cc_final: 0.8449 (tp30) REVERT: E 341 ILE cc_start: 0.9053 (mm) cc_final: 0.8769 (mp) REVERT: A 31 GLN cc_start: 0.8487 (mt0) cc_final: 0.8269 (mt0) REVERT: A 199 ASP cc_start: 0.8908 (m-30) cc_final: 0.8600 (m-30) REVERT: A 218 ASP cc_start: 0.8740 (t0) cc_final: 0.8324 (t0) REVERT: A 276 ILE cc_start: 0.8856 (tt) cc_final: 0.8530 (pp) REVERT: A 339 ARG cc_start: 0.8298 (tpp-160) cc_final: 0.7950 (tmm160) REVERT: A 341 ILE cc_start: 0.9153 (mm) cc_final: 0.8861 (mp) REVERT: A 377 MET cc_start: 0.8284 (tpp) cc_final: 0.7951 (tpt) REVERT: A 420 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7963 (mt-10) REVERT: A 434 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8301 (tp30) REVERT: B 1 MET cc_start: 0.7879 (mpm) cc_final: 0.7470 (mmm) REVERT: B 86 ARG cc_start: 0.6292 (OUTLIER) cc_final: 0.3986 (ttm-80) REVERT: B 175 VAL cc_start: 0.8578 (t) cc_final: 0.8351 (m) REVERT: B 205 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8168 (mp0) REVERT: B 320 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.8395 (mmm-85) REVERT: B 412 GLU cc_start: 0.7809 (tp30) cc_final: 0.7563 (tp30) REVERT: B 423 GLN cc_start: 0.8480 (tp40) cc_final: 0.8173 (tp40) REVERT: K 20 MET cc_start: 0.7327 (mpp) cc_final: 0.7048 (mmt) REVERT: K 63 GLU cc_start: 0.2608 (mt-10) cc_final: 0.1964 (tm-30) REVERT: K 64 ASP cc_start: 0.7369 (t0) cc_final: 0.7158 (t0) REVERT: K 147 MET cc_start: 0.4958 (tpt) cc_final: 0.4330 (tpp) REVERT: K 265 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7647 (pp) REVERT: K 266 LYS cc_start: 0.8712 (mmtt) cc_final: 0.8470 (mmtt) REVERT: K 273 LYS cc_start: 0.8750 (tmmt) cc_final: 0.8467 (pptt) REVERT: K 346 ARG cc_start: 0.7758 (ttp-110) cc_final: 0.7284 (tpm170) outliers start: 35 outliers final: 24 residues processed: 265 average time/residue: 0.5734 time to fit residues: 167.4720 Evaluate side-chains 268 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 241 SER 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 86 ARG 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 366 THR Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 293 ASN Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain K residue 337 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 22 optimal weight: 2.9990 chunk 110 optimal weight: 0.0060 chunk 142 optimal weight: 9.9990 chunk 95 optimal weight: 0.1980 chunk 69 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 147 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 157 optimal weight: 20.0000 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 176 GLN E 256 GLN ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.149848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.104721 restraints weight = 19167.040| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.38 r_work: 0.3382 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13624 Z= 0.113 Angle : 0.646 13.408 18496 Z= 0.310 Chirality : 0.044 0.285 2029 Planarity : 0.005 0.097 2402 Dihedral : 9.278 131.875 1986 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.88 % Allowed : 21.74 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.21), residues: 1671 helix: 1.78 (0.20), residues: 706 sheet: 0.39 (0.27), residues: 316 loop : -1.03 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 422 TYR 0.017 0.001 TYR K 338 PHE 0.011 0.001 PHE K 221 TRP 0.022 0.002 TRP B 344 HIS 0.002 0.000 HIS K 84 Details of bonding type rmsd covalent geometry : bond 0.00248 (13624) covalent geometry : angle 0.64640 (18496) hydrogen bonds : bond 0.03464 ( 636) hydrogen bonds : angle 4.03366 ( 1908) ********************** REFINEMENT MACRO_CYCLE 10 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 279 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 252 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.8584 (tt0) cc_final: 0.8372 (tt0) REVERT: E 128 GLN cc_start: 0.8474 (tm130) cc_final: 0.8219 (tt0) REVERT: E 341 ILE cc_start: 0.9021 (mm) cc_final: 0.8730 (mp) REVERT: A 31 GLN cc_start: 0.8464 (mt0) cc_final: 0.8222 (mt0) REVERT: A 199 ASP cc_start: 0.8898 (m-30) cc_final: 0.8602 (m-30) REVERT: A 218 ASP cc_start: 0.8692 (t0) cc_final: 0.8292 (t0) REVERT: A 276 ILE cc_start: 0.8835 (tt) cc_final: 0.8554 (pp) REVERT: A 339 ARG cc_start: 0.8210 (tpp-160) cc_final: 0.7925 (tmm160) REVERT: A 341 ILE cc_start: 0.9137 (mm) cc_final: 0.8850 (mp) REVERT: A 377 MET cc_start: 0.8307 (tpp) cc_final: 0.7933 (tpt) REVERT: A 420 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8048 (mt-10) REVERT: A 434 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8256 (tp30) REVERT: B 1 MET cc_start: 0.7911 (mpm) cc_final: 0.7440 (mmm) REVERT: B 86 ARG cc_start: 0.6232 (OUTLIER) cc_final: 0.3984 (ttm-80) REVERT: B 147 MET cc_start: 0.8222 (mmm) cc_final: 0.7970 (ttp) REVERT: B 412 GLU cc_start: 0.7781 (tp30) cc_final: 0.7537 (tp30) REVERT: B 423 GLN cc_start: 0.8475 (tp40) cc_final: 0.8155 (tp40) REVERT: K 20 MET cc_start: 0.7373 (mpp) cc_final: 0.7122 (mmt) REVERT: K 63 GLU cc_start: 0.2701 (mt-10) cc_final: 0.1993 (tm-30) REVERT: K 147 MET cc_start: 0.4828 (tpt) cc_final: 0.4120 (tpp) REVERT: K 181 LEU cc_start: 0.6803 (tm) cc_final: 0.6541 (mt) REVERT: K 273 LYS cc_start: 0.8758 (tmmt) cc_final: 0.8516 (pptt) REVERT: K 346 ARG cc_start: 0.7811 (ttp-110) cc_final: 0.7364 (tpm170) outliers start: 27 outliers final: 22 residues processed: 265 average time/residue: 0.5873 time to fit residues: 170.9429 Evaluate side-chains 259 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 241 SER 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 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 86 ARG 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 366 THR Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 293 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 114 optimal weight: 0.3980 chunk 61 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 153 optimal weight: 50.0000 chunk 154 optimal weight: 10.0000 chunk 149 optimal weight: 0.1980 chunk 91 optimal weight: 0.7980 chunk 109 optimal weight: 0.0370 chunk 26 optimal weight: 0.0670 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4274 r_free = 0.4274 target = 0.151091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.106689 restraints weight = 19076.673| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.36 r_work: 0.3406 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13624 Z= 0.112 Angle : 0.658 13.262 18496 Z= 0.316 Chirality : 0.044 0.284 2029 Planarity : 0.005 0.100 2402 Dihedral : 9.174 132.284 1986 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.95 % Allowed : 22.02 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.21), residues: 1671 helix: 1.76 (0.20), residues: 712 sheet: 0.34 (0.27), residues: 319 loop : -1.00 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 422 TYR 0.016 0.001 TYR A 24 PHE 0.017 0.001 PHE B 212 TRP 0.023 0.001 TRP B 344 HIS 0.002 0.000 HIS K 84 Details of bonding type rmsd covalent geometry : bond 0.00246 (13624) covalent geometry : angle 0.65756 (18496) hydrogen bonds : bond 0.03340 ( 636) hydrogen bonds : angle 3.99151 ( 1908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6048.58 seconds wall clock time: 103 minutes 57.10 seconds (6237.10 seconds total)