Starting phenix.real_space_refine on Sat Oct 12 20:47:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utv_42551/10_2024/8utv_42551.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utv_42551/10_2024/8utv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utv_42551/10_2024/8utv_42551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utv_42551/10_2024/8utv_42551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utv_42551/10_2024/8utv_42551.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8utv_42551/10_2024/8utv_42551.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 2 5.21 5 S 87 5.16 5 C 8346 2.51 5 N 2277 2.21 5 O 2615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 13337 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3524 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 20, 'TRANS': 430} Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3411 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 413} Chain: "K" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2782 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 11, 'TRANS': 342} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.45, per 1000 atoms: 0.71 Number of scatterers: 13337 At special positions: 0 Unit cell: (108.624, 78.84, 155.052, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 87 16.00 P 10 15.00 Mg 2 11.99 O 2615 8.00 N 2277 7.00 C 8346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.7 seconds 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3114 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 14 sheets defined 48.7% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 37 through 43 Processing helix chain 'E' and resid 71 through 81 removed outlier: 4.466A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 86 removed outlier: 4.693A pdb=" N GLN E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 113 through 129 removed outlier: 3.867A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.209A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.581A pdb=" N ASN E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.769A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 277 through 282 removed outlier: 3.960A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.678A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 removed outlier: 3.510A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 3.961A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.976A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 436 Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.530A pdb=" N THR A 41 " --> pdb=" O PRO A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.652A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 4.642A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 113 through 129 removed outlier: 3.815A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.247A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.534A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.741A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.898A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.770A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.955A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.027A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 436 Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.636A pdb=" N VAL B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.356A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.640A pdb=" N PHE B 85 " --> pdb=" O GLY B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.837A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.613A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.566A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 Processing helix chain 'B' and resid 249 through 258 removed outlier: 3.522A pdb=" N LEU B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 removed outlier: 4.128A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.918A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.230A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.792A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 69 through 77 Processing helix chain 'K' and resid 77 through 87 Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 117 through 133 Processing helix chain 'K' and resid 188 through 201 Processing helix chain 'K' and resid 262 through 296 Proline residue: K 292 - end of helix Processing helix chain 'K' and resid 309 through 315 removed outlier: 3.653A pdb=" N TRP K 313 " --> pdb=" O SER K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 320 Processing helix chain 'K' and resid 337 through 350 removed outlier: 4.180A pdb=" N ARG K 350 " --> pdb=" O ARG K 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.291A pdb=" N GLU E 3 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLN E 133 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU E 167 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'E' and resid 269 through 272 Processing sheet with id=AA4, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.268A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 removed outlier: 8.341A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN B 165 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 267 through 271 Processing sheet with id=AB1, first strand: chain 'K' and resid 54 through 56 removed outlier: 3.524A pdb=" N LYS K 7 " --> pdb=" O THR K 325 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET K 327 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL K 91 " --> pdb=" O SER K 245 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL K 247 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE K 93 " --> pdb=" O VAL K 247 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 56 removed outlier: 3.524A pdb=" N LYS K 7 " --> pdb=" O THR K 325 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET K 327 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL K 91 " --> pdb=" O SER K 245 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL K 247 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE K 93 " --> pdb=" O VAL K 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 28 through 31 Processing sheet with id=AB4, first strand: chain 'K' and resid 168 through 171 Processing sheet with id=AB5, first strand: chain 'K' and resid 205 through 206 670 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 3.72 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: 16.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 32.100 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 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:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 13624 Z= 0.337 Angle : 0.853 11.393 18496 Z= 0.465 Chirality : 0.049 0.263 2029 Planarity : 0.007 0.117 2402 Dihedral : 17.975 152.243 5113 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.07 % Favored : 95.87 % Rotamer: Outliers : 0.70 % Allowed : 13.24 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1671 helix: 1.01 (0.20), residues: 686 sheet: -0.01 (0.28), residues: 302 loop : -1.18 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 346 HIS 0.003 0.001 HIS A 88 PHE 0.021 0.002 PHE B 367 TYR 0.051 0.002 TYR A 24 ARG 0.017 0.001 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 303 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 49 PHE cc_start: 0.7313 (m-80) cc_final: 0.7110 (m-80) REVERT: E 190 THR cc_start: 0.8917 (p) cc_final: 0.8471 (t) REVERT: A 154 MET cc_start: 0.8333 (mmm) cc_final: 0.7950 (mmm) REVERT: A 190 THR cc_start: 0.8910 (p) cc_final: 0.8351 (t) REVERT: A 218 ASP cc_start: 0.8108 (t0) cc_final: 0.7877 (t0) REVERT: A 398 MET cc_start: 0.7921 (mtt) cc_final: 0.7719 (mtt) REVERT: B 14 ASN cc_start: 0.7896 (m-40) cc_final: 0.7623 (m-40) REVERT: K 149 ILE cc_start: 0.7993 (mm) cc_final: 0.7579 (mm) REVERT: K 337 ASN cc_start: 0.6689 (m110) cc_final: 0.5864 (t0) outliers start: 10 outliers final: 3 residues processed: 310 average time/residue: 1.3426 time to fit residues: 453.4144 Evaluate side-chains 247 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 244 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain K residue 132 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 50.0000 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 0.0770 chunk 97 optimal weight: 0.3980 chunk 151 optimal weight: 30.0000 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 358 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 204 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13624 Z= 0.201 Angle : 0.650 10.152 18496 Z= 0.318 Chirality : 0.046 0.291 2029 Planarity : 0.005 0.091 2402 Dihedral : 13.307 157.451 1991 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.21 % Allowed : 14.22 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1671 helix: 1.33 (0.20), residues: 709 sheet: 0.34 (0.29), residues: 302 loop : -1.09 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 344 HIS 0.004 0.001 HIS K 84 PHE 0.018 0.001 PHE K 221 TYR 0.047 0.002 TYR A 24 ARG 0.006 0.001 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 282 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 ASP cc_start: 0.7967 (m-30) cc_final: 0.7754 (m-30) REVERT: E 313 MET cc_start: 0.8297 (mtm) cc_final: 0.8064 (mtp) REVERT: A 155 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7508 (mt-10) REVERT: A 214 ARG cc_start: 0.8683 (ttp-170) cc_final: 0.8450 (tmm-80) REVERT: A 218 ASP cc_start: 0.8201 (t0) cc_final: 0.7917 (t0) REVERT: A 434 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7513 (tp30) REVERT: B 86 ARG cc_start: 0.5901 (tpt170) cc_final: 0.3926 (ttp-110) REVERT: B 208 TYR cc_start: 0.8723 (m-10) cc_final: 0.8452 (m-10) REVERT: K 48 LYS cc_start: 0.8348 (mmtm) cc_final: 0.8118 (mppt) REVERT: K 63 GLU cc_start: 0.3070 (mt-10) cc_final: 0.1761 (tm-30) REVERT: K 122 LEU cc_start: 0.7070 (mt) cc_final: 0.6848 (mp) REVERT: K 147 MET cc_start: 0.5717 (tpt) cc_final: 0.5286 (tpt) REVERT: K 223 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7322 (pp) REVERT: K 265 LEU cc_start: 0.7905 (pp) cc_final: 0.7471 (pp) REVERT: K 335 ASP cc_start: 0.6582 (OUTLIER) cc_final: 0.6013 (m-30) REVERT: K 337 ASN cc_start: 0.6719 (m110) cc_final: 0.6093 (t0) outliers start: 46 outliers final: 15 residues processed: 304 average time/residue: 1.1916 time to fit residues: 399.4094 Evaluate side-chains 257 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 239 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 A residue 155 GLU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 335 ASP Chi-restraints excluded: chain K residue 336 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 164 optimal weight: 40.0000 chunk 135 optimal weight: 20.0000 chunk 150 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 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 356 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2134 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= 0.320 Angle : 0.668 16.946 18496 Z= 0.326 Chirality : 0.048 0.489 2029 Planarity : 0.005 0.084 2402 Dihedral : 11.432 154.757 1988 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.21 % Allowed : 16.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 1671 helix: 1.42 (0.20), residues: 709 sheet: 0.42 (0.29), residues: 293 loop : -1.22 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 346 HIS 0.005 0.001 HIS E 88 PHE 0.017 0.002 PHE E 255 TYR 0.030 0.002 TYR A 24 ARG 0.007 0.001 ARG E 422 *********************** 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 312 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 266 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.7779 (tt0) cc_final: 0.7550 (tt0) REVERT: E 341 ILE cc_start: 0.9038 (mm) cc_final: 0.8788 (mp) REVERT: A 155 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7541 (mt-10) REVERT: A 214 ARG cc_start: 0.8702 (ttp-170) cc_final: 0.8469 (tmm-80) REVERT: A 218 ASP cc_start: 0.8234 (t0) cc_final: 0.7922 (t0) REVERT: A 313 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8326 (mtp) REVERT: A 434 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7472 (tp30) REVERT: B 86 ARG cc_start: 0.5740 (tpt170) cc_final: 0.3862 (ttm-80) REVERT: B 162 ARG cc_start: 0.8542 (mpt90) cc_final: 0.8161 (mmp-170) REVERT: B 230 SER cc_start: 0.9016 (m) cc_final: 0.8500 (p) REVERT: B 412 GLU cc_start: 0.7521 (tp30) cc_final: 0.7319 (tp30) REVERT: K 63 GLU cc_start: 0.3177 (mt-10) cc_final: 0.2023 (tm-30) REVERT: K 147 MET cc_start: 0.5098 (tpt) cc_final: 0.4787 (tpt) REVERT: K 264 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6956 (ppp80) REVERT: K 273 LYS cc_start: 0.8563 (tmmt) cc_final: 0.8267 (pptt) REVERT: K 315 LEU cc_start: 0.8810 (mm) cc_final: 0.8363 (tm) REVERT: K 337 ASN cc_start: 0.6623 (m110) cc_final: 0.6063 (t0) outliers start: 46 outliers final: 24 residues processed: 284 average time/residue: 1.2143 time to fit residues: 379.3328 Evaluate side-chains 266 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 239 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 285 GLN Chi-restraints excluded: chain E residue 337 THR 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 321 MET 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 132 ASP Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 264 ARG Chi-restraints excluded: chain K residue 293 ASN Chi-restraints excluded: chain K residue 335 ASP Chi-restraints excluded: chain K residue 336 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 20.0000 chunk 114 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 144 optimal weight: 20.0000 chunk 43 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 256 GLN A 102 ASN A 256 GLN A 356 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 347 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13624 Z= 0.182 Angle : 0.642 17.824 18496 Z= 0.304 Chirality : 0.046 0.456 2029 Planarity : 0.004 0.081 2402 Dihedral : 10.521 154.963 1988 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.86 % Allowed : 17.21 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1671 helix: 1.55 (0.20), residues: 713 sheet: 0.26 (0.29), residues: 311 loop : -1.17 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.005 0.001 HIS A 192 PHE 0.014 0.001 PHE K 221 TYR 0.026 0.001 TYR K 105 ARG 0.006 0.000 ARG B 320 *********************** 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 300 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 259 time to evaluate : 1.760 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: 0.7800 (tt0) cc_final: 0.7582 (tt0) REVERT: E 341 ILE cc_start: 0.8999 (mm) cc_final: 0.8743 (mp) REVERT: E 434 GLU cc_start: 0.7644 (tt0) cc_final: 0.7427 (mt-10) REVERT: A 214 ARG cc_start: 0.8675 (ttp-170) cc_final: 0.8467 (tmm-80) REVERT: A 218 ASP cc_start: 0.8228 (t0) cc_final: 0.7942 (t0) REVERT: A 276 ILE cc_start: 0.8536 (tt) cc_final: 0.8301 (pp) REVERT: A 341 ILE cc_start: 0.9124 (mm) cc_final: 0.8869 (mp) REVERT: A 434 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7492 (tp30) REVERT: B 86 ARG cc_start: 0.5750 (tpt170) cc_final: 0.3914 (ttm-80) REVERT: B 412 GLU cc_start: 0.7467 (tp30) cc_final: 0.7081 (tp30) REVERT: B 423 GLN cc_start: 0.8221 (tp40) cc_final: 0.7998 (tp40) REVERT: K 63 GLU cc_start: 0.3064 (mt-10) cc_final: 0.2071 (tm-30) REVERT: K 147 MET cc_start: 0.4949 (tpt) cc_final: 0.4677 (tpt) REVERT: K 223 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7260 (pp) REVERT: K 264 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6907 (ppp80) REVERT: K 273 LYS cc_start: 0.8560 (tmmt) cc_final: 0.8322 (pptt) REVERT: K 335 ASP cc_start: 0.6706 (OUTLIER) cc_final: 0.6012 (m-30) REVERT: K 337 ASN cc_start: 0.6716 (m110) cc_final: 0.6359 (t0) outliers start: 41 outliers final: 18 residues processed: 277 average time/residue: 1.1694 time to fit residues: 356.8783 Evaluate side-chains 262 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 241 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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 198 SER 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 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 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 264 ARG Chi-restraints excluded: chain K residue 293 ASN Chi-restraints excluded: chain K residue 335 ASP Chi-restraints excluded: chain K residue 336 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 50.0000 chunk 91 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 137 optimal weight: 0.0670 chunk 111 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 301 GLN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13624 Z= 0.278 Angle : 0.656 17.723 18496 Z= 0.312 Chirality : 0.047 0.370 2029 Planarity : 0.004 0.077 2402 Dihedral : 10.290 151.558 1988 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.69 % Allowed : 17.70 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1671 helix: 1.57 (0.20), residues: 707 sheet: 0.27 (0.28), residues: 318 loop : -1.17 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 21 HIS 0.005 0.001 HIS A 192 PHE 0.015 0.002 PHE K 221 TYR 0.029 0.002 TYR K 105 ARG 0.010 0.000 ARG E 339 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 255 time to evaluate : 1.518 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 341 ILE cc_start: 0.9023 (mm) cc_final: 0.8769 (mp) REVERT: A 218 ASP cc_start: 0.8233 (t0) cc_final: 0.7717 (t0) REVERT: A 276 ILE cc_start: 0.8581 (tt) cc_final: 0.8351 (pp) REVERT: A 434 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7583 (tp30) REVERT: B 86 ARG cc_start: 0.5765 (tpt170) cc_final: 0.3864 (ttm-80) REVERT: B 179 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8864 (t) REVERT: B 230 SER cc_start: 0.8986 (m) cc_final: 0.8482 (p) REVERT: B 412 GLU cc_start: 0.7499 (tp30) cc_final: 0.7226 (tp30) REVERT: B 423 GLN cc_start: 0.8251 (tp40) cc_final: 0.7991 (tp40) REVERT: K 63 GLU cc_start: 0.3183 (mt-10) cc_final: 0.2200 (tm-30) REVERT: K 122 LEU cc_start: 0.6387 (OUTLIER) cc_final: 0.6174 (mm) REVERT: K 126 LEU cc_start: 0.8859 (mt) cc_final: 0.8402 (pp) REVERT: K 147 MET cc_start: 0.4796 (tpt) cc_final: 0.4390 (tpt) REVERT: K 264 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6921 (ppp80) REVERT: K 266 LYS cc_start: 0.8698 (mmtp) cc_final: 0.8475 (mmtt) REVERT: K 273 LYS cc_start: 0.8559 (tmmt) cc_final: 0.8300 (pptt) REVERT: K 337 ASN cc_start: 0.6715 (m110) cc_final: 0.6294 (t0) outliers start: 53 outliers final: 30 residues processed: 281 average time/residue: 1.1575 time to fit residues: 358.1975 Evaluate side-chains 279 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 246 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 198 SER Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 285 GLN Chi-restraints excluded: chain E residue 337 THR 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 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 179 VAL 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 73 VAL Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 264 ARG Chi-restraints excluded: chain K residue 271 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 54 optimal weight: 8.9990 chunk 145 optimal weight: 30.0000 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 134 optimal weight: 50.0000 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 256 GLN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13624 Z= 0.293 Angle : 0.669 19.080 18496 Z= 0.322 Chirality : 0.047 0.356 2029 Planarity : 0.004 0.076 2402 Dihedral : 10.397 146.199 1988 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.41 % Allowed : 18.68 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1671 helix: 1.50 (0.20), residues: 708 sheet: 0.24 (0.28), residues: 315 loop : -1.18 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 344 HIS 0.004 0.001 HIS K 218 PHE 0.013 0.002 PHE E 49 TYR 0.036 0.002 TYR K 105 ARG 0.007 0.000 ARG B 320 *********************** 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 312 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 263 time to evaluate : 1.528 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 128 GLN cc_start: 0.8372 (tm130) cc_final: 0.8158 (tt0) REVERT: E 341 ILE cc_start: 0.9015 (mm) cc_final: 0.8755 (mp) REVERT: A 218 ASP cc_start: 0.8186 (t0) cc_final: 0.7689 (t0) REVERT: A 434 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7593 (tp30) REVERT: B 1 MET cc_start: 0.6156 (mpm) cc_final: 0.5924 (mmm) REVERT: B 86 ARG cc_start: 0.5733 (tpt170) cc_final: 0.3850 (ttm-80) REVERT: B 179 VAL cc_start: 0.9081 (OUTLIER) cc_final: 0.8876 (t) REVERT: B 230 SER cc_start: 0.8995 (m) cc_final: 0.8569 (p) REVERT: B 412 GLU cc_start: 0.7483 (tp30) cc_final: 0.7206 (tp30) REVERT: B 423 GLN cc_start: 0.8247 (tp40) cc_final: 0.8017 (tp40) REVERT: K 63 GLU cc_start: 0.3184 (mt-10) cc_final: 0.2285 (tm-30) REVERT: K 122 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5957 (mm) REVERT: K 126 LEU cc_start: 0.8847 (mt) cc_final: 0.8434 (pp) REVERT: K 147 MET cc_start: 0.4557 (tpt) cc_final: 0.4142 (tpt) REVERT: K 177 TYR cc_start: 0.7501 (p90) cc_final: 0.6532 (p90) REVERT: K 223 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7215 (pp) REVERT: K 273 LYS cc_start: 0.8616 (tmmt) cc_final: 0.8381 (pptt) REVERT: K 337 ASN cc_start: 0.6857 (m110) cc_final: 0.6434 (t0) outliers start: 49 outliers final: 32 residues processed: 285 average time/residue: 1.3067 time to fit residues: 409.6537 Evaluate side-chains 287 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 252 time to evaluate : 1.545 ------------------------------------------------------------------------------- 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 198 SER Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 285 GLN Chi-restraints excluded: chain E residue 337 THR 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 A residue 437 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 209 ASP 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 429 THR Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 50.0000 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 117 optimal weight: 0.0040 chunk 91 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 160 optimal weight: 20.0000 chunk 100 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 74 optimal weight: 0.3980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 ASN E 256 GLN ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN A 356 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2910 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= 0.178 Angle : 0.644 17.214 18496 Z= 0.305 Chirality : 0.044 0.260 2029 Planarity : 0.004 0.076 2402 Dihedral : 9.693 139.314 1988 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.93 % Allowed : 19.72 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.21), residues: 1671 helix: 1.67 (0.20), residues: 708 sheet: 0.25 (0.28), residues: 318 loop : -1.07 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 344 HIS 0.003 0.001 HIS A 192 PHE 0.013 0.001 PHE A 52 TYR 0.035 0.001 TYR K 105 ARG 0.009 0.000 ARG E 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 280 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 128 GLN cc_start: 0.8300 (tm130) cc_final: 0.8061 (tt0) REVERT: E 341 ILE cc_start: 0.8957 (mm) cc_final: 0.8695 (mp) REVERT: A 199 ASP cc_start: 0.8525 (m-30) cc_final: 0.8218 (m-30) REVERT: A 214 ARG cc_start: 0.8661 (ttp-170) cc_final: 0.8439 (tmm-80) REVERT: A 218 ASP cc_start: 0.8165 (t0) cc_final: 0.7665 (t0) REVERT: A 341 ILE cc_start: 0.9112 (mm) cc_final: 0.8844 (mp) REVERT: A 434 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7534 (tp30) REVERT: B 1 MET cc_start: 0.6116 (mpm) cc_final: 0.5906 (mmm) REVERT: B 86 ARG cc_start: 0.5713 (tpt170) cc_final: 0.3845 (ttm-80) REVERT: B 230 SER cc_start: 0.8960 (m) cc_final: 0.8566 (p) REVERT: B 412 GLU cc_start: 0.7460 (tp30) cc_final: 0.7238 (tp30) REVERT: B 423 GLN cc_start: 0.8210 (tp40) cc_final: 0.7926 (tp40) REVERT: K 20 MET cc_start: 0.6927 (mpp) cc_final: 0.6465 (mmt) REVERT: K 63 GLU cc_start: 0.3243 (mt-10) cc_final: 0.2333 (tm-30) REVERT: K 147 MET cc_start: 0.4621 (tpt) cc_final: 0.4049 (tpt) REVERT: K 177 TYR cc_start: 0.7513 (p90) cc_final: 0.6568 (p90) REVERT: K 223 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7176 (pp) REVERT: K 273 LYS cc_start: 0.8628 (tmmt) cc_final: 0.8406 (pptt) REVERT: K 337 ASN cc_start: 0.6732 (m110) cc_final: 0.6249 (t0) outliers start: 42 outliers final: 24 residues processed: 300 average time/residue: 1.1125 time to fit residues: 372.6118 Evaluate side-chains 284 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 259 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 170 SER 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 312 THR 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 46 THR Chi-restraints excluded: chain K residue 73 VAL 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 271 ILE Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 293 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 146 optimal weight: 40.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 102 ASN E 176 GLN E 256 GLN ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN A 342 GLN A 356 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13624 Z= 0.198 Angle : 0.689 17.925 18496 Z= 0.323 Chirality : 0.046 0.442 2029 Planarity : 0.004 0.076 2402 Dihedral : 9.551 134.638 1988 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.51 % Allowed : 21.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.21), residues: 1671 helix: 1.66 (0.20), residues: 708 sheet: 0.30 (0.27), residues: 318 loop : -1.08 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 344 HIS 0.004 0.001 HIS A 192 PHE 0.025 0.001 PHE E 255 TYR 0.039 0.001 TYR K 105 ARG 0.010 0.000 ARG E 339 *********************** 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 307 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 271 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 128 GLN cc_start: 0.8281 (tm130) cc_final: 0.8039 (tt0) REVERT: E 341 ILE cc_start: 0.8942 (mm) cc_final: 0.8681 (mp) REVERT: A 31 GLN cc_start: 0.8186 (mt0) cc_final: 0.7936 (mt0) REVERT: A 168 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7646 (mm-30) REVERT: A 214 ARG cc_start: 0.8666 (ttp-170) cc_final: 0.8439 (tmm-80) REVERT: A 218 ASP cc_start: 0.8122 (t0) cc_final: 0.7657 (t0) REVERT: A 276 ILE cc_start: 0.8625 (tt) cc_final: 0.8334 (pp) REVERT: A 434 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7433 (tp30) REVERT: B 1 MET cc_start: 0.6156 (mpm) cc_final: 0.5936 (mmm) REVERT: B 86 ARG cc_start: 0.5720 (OUTLIER) cc_final: 0.3874 (ttm-80) REVERT: B 412 GLU cc_start: 0.7450 (tp30) cc_final: 0.7216 (tp30) REVERT: B 423 GLN cc_start: 0.8206 (tp40) cc_final: 0.7924 (tp40) REVERT: K 20 MET cc_start: 0.6947 (mpp) cc_final: 0.6583 (mmt) REVERT: K 63 GLU cc_start: 0.3269 (mt-10) cc_final: 0.2448 (tm-30) REVERT: K 147 MET cc_start: 0.4504 (tpt) cc_final: 0.3845 (tpt) REVERT: K 177 TYR cc_start: 0.7486 (p90) cc_final: 0.6575 (p90) REVERT: K 181 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5786 (mt) REVERT: K 223 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7237 (pp) REVERT: K 335 ASP cc_start: 0.6747 (m-30) cc_final: 0.6427 (m-30) REVERT: K 337 ASN cc_start: 0.6700 (m110) cc_final: 0.6253 (t0) outliers start: 36 outliers final: 25 residues processed: 286 average time/residue: 1.0810 time to fit residues: 342.5067 Evaluate side-chains 278 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 250 time to evaluate : 1.476 ------------------------------------------------------------------------------- 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 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 429 THR Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 271 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 46 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 141 optimal weight: 50.0000 chunk 98 optimal weight: 0.9990 chunk 158 optimal weight: 8.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 ASN E 176 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN A 192 HIS A 356 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 165 ASN B 347 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 13624 Z= 0.529 Angle : 0.788 17.071 18496 Z= 0.384 Chirality : 0.052 0.447 2029 Planarity : 0.005 0.094 2402 Dihedral : 10.182 140.783 1986 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.07 % Allowed : 21.05 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1671 helix: 1.35 (0.20), residues: 701 sheet: 0.22 (0.27), residues: 320 loop : -1.21 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 101 HIS 0.010 0.001 HIS E 88 PHE 0.022 0.002 PHE E 49 TYR 0.038 0.002 TYR K 105 ARG 0.017 0.001 ARG A 422 *********************** 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 306 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 262 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 128 GLN cc_start: 0.8373 (tm130) cc_final: 0.8157 (tt0) REVERT: E 190 THR cc_start: 0.8952 (p) cc_final: 0.8485 (t) REVERT: A 190 THR cc_start: 0.8944 (p) cc_final: 0.8710 (p) REVERT: A 218 ASP cc_start: 0.8186 (t0) cc_final: 0.7677 (t0) REVERT: A 392 ASP cc_start: 0.8097 (t70) cc_final: 0.7865 (t0) REVERT: A 434 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7410 (tp30) REVERT: A 437 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8269 (p) REVERT: B 86 ARG cc_start: 0.5639 (tpt170) cc_final: 0.3734 (ttm110) REVERT: B 298 ASN cc_start: 0.8844 (t0) cc_final: 0.8601 (t0) REVERT: B 412 GLU cc_start: 0.7512 (tp30) cc_final: 0.7225 (tp30) REVERT: B 423 GLN cc_start: 0.8289 (tp40) cc_final: 0.8033 (tp40) REVERT: K 63 GLU cc_start: 0.3187 (mt-10) cc_final: 0.2414 (tm-30) REVERT: K 81 MET cc_start: 0.3946 (OUTLIER) cc_final: 0.3493 (mmt) REVERT: K 147 MET cc_start: 0.4030 (tpt) cc_final: 0.3313 (tpt) REVERT: K 223 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7228 (pp) REVERT: K 346 ARG cc_start: 0.7638 (ttp-110) cc_final: 0.7142 (tpm170) outliers start: 44 outliers final: 26 residues processed: 281 average time/residue: 1.1213 time to fit residues: 348.6124 Evaluate side-chains 277 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 248 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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 122 ILE Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 170 SER 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 437 VAL Chi-restraints excluded: chain A residue 9 VAL 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 A residue 437 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 223 ILE Chi-restraints excluded: chain K residue 271 ILE Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 336 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 166 optimal weight: 8.9990 chunk 153 optimal weight: 30.0000 chunk 132 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 0.2980 chunk 81 optimal weight: 0.1980 chunk 105 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN A 128 GLN A 139 HIS A 356 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13624 Z= 0.189 Angle : 0.698 17.330 18496 Z= 0.331 Chirality : 0.046 0.452 2029 Planarity : 0.005 0.080 2402 Dihedral : 9.618 135.104 1986 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.67 % Allowed : 23.14 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1671 helix: 1.54 (0.20), residues: 704 sheet: 0.19 (0.27), residues: 317 loop : -1.08 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 344 HIS 0.003 0.000 HIS K 218 PHE 0.018 0.001 PHE B 212 TYR 0.042 0.001 TYR K 105 ARG 0.017 0.001 ARG A 422 ********************** 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 282 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 258 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 128 GLN cc_start: 0.8274 (tm130) cc_final: 0.8054 (tt0) REVERT: E 339 ARG cc_start: 0.7661 (tpp-160) cc_final: 0.7101 (mmp80) REVERT: E 341 ILE cc_start: 0.8976 (mm) cc_final: 0.8716 (mp) REVERT: A 31 GLN cc_start: 0.8177 (mt0) cc_final: 0.7968 (mt0) REVERT: A 199 ASP cc_start: 0.8501 (m-30) cc_final: 0.8205 (m-30) REVERT: A 214 ARG cc_start: 0.8667 (ttp-170) cc_final: 0.8452 (tmm-80) REVERT: A 218 ASP cc_start: 0.8091 (t0) cc_final: 0.7634 (t0) REVERT: A 276 ILE cc_start: 0.8625 (tt) cc_final: 0.8331 (pp) REVERT: A 434 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7468 (tp30) REVERT: B 86 ARG cc_start: 0.5706 (tpt170) cc_final: 0.3890 (ttm110) REVERT: B 366 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.7910 (p) REVERT: B 412 GLU cc_start: 0.7473 (tp30) cc_final: 0.7270 (tp30) REVERT: B 423 GLN cc_start: 0.8220 (tp40) cc_final: 0.7960 (tp40) REVERT: K 147 MET cc_start: 0.4236 (tpt) cc_final: 0.3552 (tpt) REVERT: K 346 ARG cc_start: 0.7625 (ttp-110) cc_final: 0.7074 (tpm170) outliers start: 24 outliers final: 21 residues processed: 270 average time/residue: 1.1306 time to fit residues: 336.5124 Evaluate side-chains 273 residues out of total 1435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 251 time to evaluate : 1.507 ------------------------------------------------------------------------------- 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 147 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 271 ILE 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 40 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 19 optimal weight: 0.0170 chunk 36 optimal weight: 0.0670 chunk 132 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 1.1758 ------------------------------------------------------------------------------- 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 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.146588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.101683 restraints weight = 19024.605| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.33 r_work: 0.3333 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13624 Z= 0.230 Angle : 0.727 16.447 18496 Z= 0.349 Chirality : 0.047 0.455 2029 Planarity : 0.005 0.081 2402 Dihedral : 9.606 132.993 1986 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.95 % Allowed : 23.14 % Favored : 74.91 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1671 helix: 1.52 (0.20), residues: 706 sheet: 0.25 (0.27), residues: 317 loop : -1.07 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 388 HIS 0.003 0.001 HIS K 218 PHE 0.015 0.001 PHE E 255 TYR 0.039 0.001 TYR K 105 ARG 0.010 0.001 ARG E 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6026.34 seconds wall clock time: 110 minutes 16.74 seconds (6616.74 seconds total)