Starting phenix.real_space_refine on Thu Aug 6 21:10:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ukg_64238/08_2026/9ukg_64238.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ukg_64238/08_2026/9ukg_64238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ukg_64238/08_2026/9ukg_64238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ukg_64238/08_2026/9ukg_64238.map" model { file = "/net/cci-nas-00/data/ceres_data/9ukg_64238/08_2026/9ukg_64238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ukg_64238/08_2026/9ukg_64238.cif" } resolution = 3.54 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= 0.002 sd= 0.033 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 6 5.49 5 Mg 2 5.21 5 S 70 5.16 5 C 10682 2.51 5 N 2995 2.21 5 O 3166 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16921 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2342 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "B" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2354 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain breaks: 1 Chain: "C" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2386 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain breaks: 1 Chain: "D" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2438 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 297} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2442 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 11, 'TRANS': 297} Chain: "F" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2456 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 12, 'TRANS': 296} Chain breaks: 1 Chain: "G" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2439 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 10, 'TRANS': 295} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.89, per 1000 atoms: 0.23 Number of scatterers: 16921 At special positions: 0 Unit cell: (117.962, 135.412, 127.734, 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 70 16.00 P 6 15.00 Mg 2 11.99 O 3166 8.00 N 2995 7.00 C 10682 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 824.1 milliseconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4004 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 25 sheets defined 46.7% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 50 through 63 Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.911A pdb=" N ILE A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.578A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 150 through 159 Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 223 through 231 removed outlier: 4.274A pdb=" N ASN A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.705A pdb=" N TYR A 236 " --> pdb=" O ALA A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 261 Processing helix chain 'A' and resid 271 through 284 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.552A pdb=" N ALA A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 298 Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.663A pdb=" N VAL A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 removed outlier: 3.509A pdb=" N GLY B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 63 Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.929A pdb=" N VAL B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 126 through 132 Processing helix chain 'B' and resid 150 through 159 removed outlier: 3.673A pdb=" N VAL B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B 158 " --> pdb=" O ILE B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 removed outlier: 3.963A pdb=" N ARG B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 233 Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 238 through 261 removed outlier: 3.983A pdb=" N GLU B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B 258 " --> pdb=" O MET B 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 284 Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 295 through 298 Processing helix chain 'B' and resid 299 through 315 removed outlier: 4.191A pdb=" N ALA B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N THR B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 63 Processing helix chain 'C' and resid 76 through 88 removed outlier: 3.525A pdb=" N ILE C 81 " --> pdb=" O LYS C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 126 through 134 Processing helix chain 'C' and resid 147 through 158 removed outlier: 4.150A pdb=" N VAL C 153 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 157 " --> pdb=" O VAL C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 221 through 232 removed outlier: 3.719A pdb=" N LYS C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 262 removed outlier: 3.927A pdb=" N GLU C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 283 Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 299 through 315 removed outlier: 4.552A pdb=" N ALA C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N THR C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 50 through 63 Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.566A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 134 removed outlier: 3.827A pdb=" N TRP D 130 " --> pdb=" O GLY D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 223 through 233 Processing helix chain 'D' and resid 238 through 262 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 286 through 294 Processing helix chain 'D' and resid 295 through 298 Processing helix chain 'D' and resid 302 through 314 removed outlier: 3.747A pdb=" N VAL D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 22 Processing helix chain 'E' and resid 50 through 64 Processing helix chain 'E' and resid 76 through 89 Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 126 through 134 Processing helix chain 'E' and resid 147 through 152 Processing helix chain 'E' and resid 206 through 210 Processing helix chain 'E' and resid 221 through 233 Processing helix chain 'E' and resid 234 through 237 removed outlier: 3.901A pdb=" N GLN E 237 " --> pdb=" O LYS E 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 234 through 237' Processing helix chain 'E' and resid 239 through 261 removed outlier: 4.079A pdb=" N GLU E 243 " --> pdb=" O ALA E 239 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE E 244 " --> pdb=" O GLU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 284 Processing helix chain 'E' and resid 285 through 294 Processing helix chain 'E' and resid 295 through 298 Processing helix chain 'E' and resid 302 through 315 removed outlier: 3.595A pdb=" N VAL E 306 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 50 through 64 Processing helix chain 'F' and resid 76 through 88 Processing helix chain 'F' and resid 102 through 107 Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 147 through 159 Processing helix chain 'F' and resid 221 through 233 Processing helix chain 'F' and resid 238 through 262 removed outlier: 3.522A pdb=" N ARG F 242 " --> pdb=" O ASN F 238 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 284 removed outlier: 3.658A pdb=" N ALA F 281 " --> pdb=" O ALA F 277 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE F 282 " --> pdb=" O GLU F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 294 removed outlier: 3.629A pdb=" N ALA F 289 " --> pdb=" O ASP F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 298 Processing helix chain 'F' and resid 299 through 302 Processing helix chain 'F' and resid 303 through 314 Processing helix chain 'G' and resid 336 through 352 removed outlier: 4.032A pdb=" N GLY G 345 " --> pdb=" O ASP G 341 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE G 346 " --> pdb=" O ARG G 342 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS G 349 " --> pdb=" O GLY G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 372 removed outlier: 3.862A pdb=" N ARG G 364 " --> pdb=" O ARG G 360 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN G 372 " --> pdb=" O ARG G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 397 removed outlier: 4.066A pdb=" N ILE G 394 " --> pdb=" O ARG G 390 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL G 395 " --> pdb=" O LEU G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 428 Processing helix chain 'G' and resid 429 through 449 removed outlier: 3.816A pdb=" N ARG G 444 " --> pdb=" O ASP G 440 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR G 445 " --> pdb=" O ILE G 441 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG G 448 " --> pdb=" O ARG G 444 " (cutoff:3.500A) Processing helix chain 'G' and resid 466 through 475 removed outlier: 3.572A pdb=" N GLU G 470 " --> pdb=" O GLY G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 505 through 510 Processing helix chain 'G' and resid 519 through 533 removed outlier: 3.823A pdb=" N ALA G 523 " --> pdb=" O ILE G 519 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY G 533 " --> pdb=" O GLN G 529 " (cutoff:3.500A) Processing helix chain 'G' and resid 551 through 558 removed outlier: 4.464A pdb=" N VAL G 557 " --> pdb=" O SER G 553 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN G 558 " --> pdb=" O THR G 554 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 577 removed outlier: 4.332A pdb=" N GLU G 564 " --> pdb=" O GLY G 560 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS G 566 " --> pdb=" O TYR G 562 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU G 573 " --> pdb=" O ALA G 569 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE G 574 " --> pdb=" O VAL G 570 " (cutoff:3.500A) Processing helix chain 'G' and resid 603 through 621 removed outlier: 3.648A pdb=" N GLY G 609 " --> pdb=" O GLU G 605 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET G 611 " --> pdb=" O LEU G 607 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR G 612 " --> pdb=" O ALA G 608 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER G 617 " --> pdb=" O GLU G 613 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU G 618 " --> pdb=" O GLN G 614 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE G 619 " --> pdb=" O LEU G 615 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU G 620 " --> pdb=" O ALA G 616 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU G 621 " --> pdb=" O SER G 617 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 96 removed outlier: 6.386A pdb=" N VAL A 93 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASP A 141 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL A 95 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU A 138 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR A 184 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE A 140 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 185 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N MET A 68 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU A 217 " --> pdb=" O MET A 68 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER A 70 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 115 removed outlier: 3.724A pdb=" N ALA A 111 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 122 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 17 Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 96 removed outlier: 6.468A pdb=" N ARG B 66 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N THR B 215 " --> pdb=" O ARG B 66 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N MET B 68 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 109 through 113 Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 96 removed outlier: 6.636A pdb=" N VAL C 67 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ALA C 185 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 69 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 109 through 115 Processing sheet with id=AB1, first strand: chain 'C' and resid 164 through 166 Processing sheet with id=AB2, first strand: chain 'D' and resid 14 through 17 Processing sheet with id=AB3, first strand: chain 'D' and resid 92 through 96 removed outlier: 3.801A pdb=" N VAL D 67 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N MET D 68 " --> pdb=" O THR D 215 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 108 through 115 Processing sheet with id=AB5, first strand: chain 'D' and resid 164 through 166 Processing sheet with id=AB6, first strand: chain 'E' and resid 14 through 17 Processing sheet with id=AB7, first strand: chain 'E' and resid 92 through 96 removed outlier: 6.112A pdb=" N LEU E 138 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N THR E 184 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE E 140 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N MET E 68 " --> pdb=" O THR E 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 108 through 115 Processing sheet with id=AB9, first strand: chain 'E' and resid 164 through 166 Processing sheet with id=AC1, first strand: chain 'F' and resid 14 through 17 Processing sheet with id=AC2, first strand: chain 'F' and resid 92 through 96 removed outlier: 6.486A pdb=" N VAL F 93 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ASP F 141 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL F 95 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU F 138 " --> pdb=" O PHE F 182 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR F 184 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE F 140 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL F 67 " --> pdb=" O ALA F 183 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ALA F 185 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL F 69 " --> pdb=" O ALA F 185 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 108 through 115 removed outlier: 3.593A pdb=" N VAL F 118 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 164 through 165 Processing sheet with id=AC5, first strand: chain 'G' and resid 327 through 329 removed outlier: 6.346A pdb=" N ILE G 455 " --> pdb=" O TYR G 492 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR G 415 " --> pdb=" O LYS G 452 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLU G 454 " --> pdb=" O THR G 415 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL G 417 " --> pdb=" O GLU G 454 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU G 456 " --> pdb=" O VAL G 417 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU G 419 " --> pdb=" O LEU G 456 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N PHE G 458 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU G 421 " --> pdb=" O PHE G 458 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N THR G 460 " --> pdb=" O LEU G 421 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL G 416 " --> pdb=" O ILE G 540 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N MET G 542 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N THR G 418 " --> pdb=" O MET G 542 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 377 through 378 Processing sheet with id=AC7, first strand: chain 'G' and resid 544 through 545 removed outlier: 3.555A pdb=" N SER G 545 " --> pdb=" O ILE G 585 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY G 586 " --> pdb=" O ILE G 601 " (cutoff:3.500A) 722 hydrogen bonds defined for protein. 2043 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: 1.99 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5720 1.34 - 1.46: 2688 1.46 - 1.57: 8722 1.57 - 1.69: 9 1.69 - 1.81: 125 Bond restraints: 17264 Sorted by residual: bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" O3A ANP E 401 " pdb=" PB ANP E 401 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 1.795 1.685 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" N3B ANP E 401 " pdb=" PG ANP E 401 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" O5' ANP E 401 " pdb=" PA ANP E 401 " ideal model delta sigma weight residual 1.655 1.578 0.077 2.00e-02 2.50e+03 1.48e+01 ... (remaining 17259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 23406 3.80 - 7.61: 61 7.61 - 11.41: 6 11.41 - 15.22: 1 15.22 - 19.02: 2 Bond angle restraints: 23476 Sorted by residual: angle pdb=" PB ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 126.95 107.93 19.02 3.00e+00 1.11e-01 4.02e+01 angle pdb=" PB ANP E 401 " pdb=" N3B ANP E 401 " pdb=" PG ANP E 401 " ideal model delta sigma weight residual 126.95 108.87 18.08 3.00e+00 1.11e-01 3.63e+01 angle pdb=" CB MET F 208 " pdb=" CG MET F 208 " pdb=" SD MET F 208 " ideal model delta sigma weight residual 112.70 124.86 -12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" CA ARG C 250 " pdb=" CB ARG C 250 " pdb=" CG ARG C 250 " ideal model delta sigma weight residual 114.10 121.69 -7.59 2.00e+00 2.50e-01 1.44e+01 angle pdb=" O1B ANP F 401 " pdb=" PB ANP F 401 " pdb=" O2B ANP F 401 " ideal model delta sigma weight residual 120.08 109.40 10.68 3.00e+00 1.11e-01 1.27e+01 ... (remaining 23471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.35: 9181 25.35 - 50.71: 986 50.71 - 76.06: 133 76.06 - 101.42: 30 101.42 - 126.77: 1 Dihedral angle restraints: 10331 sinusoidal: 4143 harmonic: 6188 Sorted by residual: dihedral pdb=" O1A ANP E 401 " pdb=" O3A ANP E 401 " pdb=" PA ANP E 401 " pdb=" PB ANP E 401 " ideal model delta sinusoidal sigma weight residual 83.11 -43.66 126.77 1 3.00e+01 1.11e-03 1.71e+01 dihedral pdb=" CA ILE D 203 " pdb=" C ILE D 203 " pdb=" N ASN D 204 " pdb=" CA ASN D 204 " ideal model delta harmonic sigma weight residual -180.00 -161.03 -18.97 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CG ARG F 51 " pdb=" CD ARG F 51 " pdb=" NE ARG F 51 " pdb=" CZ ARG F 51 " ideal model delta sinusoidal sigma weight residual 90.00 39.97 50.03 2 1.50e+01 4.44e-03 1.25e+01 ... (remaining 10328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2182 0.056 - 0.112: 433 0.112 - 0.168: 39 0.168 - 0.224: 1 0.224 - 0.279: 2 Chirality restraints: 2657 Sorted by residual: chirality pdb=" C3' ANP E 401 " pdb=" C2' ANP E 401 " pdb=" C4' ANP E 401 " pdb=" O3' ANP E 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C3' ANP F 401 " pdb=" C2' ANP F 401 " pdb=" C4' ANP F 401 " pdb=" O3' ANP F 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA VAL D 150 " pdb=" N VAL D 150 " pdb=" C VAL D 150 " pdb=" CB VAL D 150 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.85e-01 ... (remaining 2654 not shown) Planarity restraints: 3058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 223 " 0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ASP D 223 " -0.057 2.00e-02 2.50e+03 pdb=" O ASP D 223 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN D 224 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 269 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO E 270 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 270 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 270 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 269 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO D 270 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 270 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 270 " 0.028 5.00e-02 4.00e+02 ... (remaining 3055 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 101 2.48 - 3.08: 11579 3.08 - 3.69: 26005 3.69 - 4.29: 36380 4.29 - 4.90: 61063 Nonbonded interactions: 135128 Sorted by model distance: nonbonded pdb=" O2G ANP F 401 " pdb="MG MG F 402 " model vdw 1.871 2.170 nonbonded pdb=" O3G ANP E 401 " pdb="MG MG E 402 " model vdw 1.912 2.170 nonbonded pdb=" O1B ANP F 401 " pdb="MG MG F 402 " model vdw 2.104 2.170 nonbonded pdb=" O1B ANP F 401 " pdb=" O2G ANP F 401 " model vdw 2.167 3.040 nonbonded pdb=" NH1 ARG B 94 " pdb=" OD2 ASP B 141 " model vdw 2.202 3.120 ... (remaining 135123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 188 or resid 204 through 310 or (resid 311 and ( \ name N or name CA or name C or name O or name CB )) or resid 312 through 315)) selection = (chain 'B' and (resid 9 through 310 or (resid 311 and (name N or name CA or name \ C or name O or name CB )) or resid 312 through 315)) selection = (chain 'C' and (resid 9 through 188 or resid 204 through 310 or (resid 311 and ( \ name N or name CA or name C or name O or name CB )) or resid 312 through 315)) selection = (chain 'D' and (resid 9 through 188 or resid 204 through 315)) selection = (chain 'E' and (resid 9 through 188 or resid 204 through 310 or (resid 311 and ( \ name N or name CA or name C or name O or name CB )) or resid 312 through 315)) selection = (chain 'F' and (resid 9 through 188 or resid 204 through 310 or (resid 311 and ( \ name N or name CA or name C or name O or name CB )) or resid 312 through 315)) } 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 group one per residue 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: 4.610 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: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.230 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 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 : 0.004 0.149 17264 Z= 0.212 Angle : 0.627 19.021 23476 Z= 0.315 Chirality : 0.043 0.279 2657 Planarity : 0.004 0.051 3058 Dihedral : 19.616 126.774 6327 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.72 % Allowed : 37.08 % Favored : 62.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.18), residues: 2103 helix: 0.10 (0.17), residues: 878 sheet: -0.67 (0.27), residues: 335 loop : -0.91 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 51 TYR 0.014 0.001 TYR D 132 PHE 0.013 0.001 PHE C 309 TRP 0.011 0.001 TRP A 211 HIS 0.011 0.001 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 (17264) covalent geometry : angle 0.62651 / 0.32 (23476) hydrogen bonds : bond 0.12966 / 9.14 ( 722) hydrogen bonds : angle 6.41303 / 4.53 ( 2043) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 450 time to evaluate : 0.431 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: C 250 ARG cc_start: 0.7836 (mmp-170) cc_final: 0.7631 (mmp-170) REVERT: E 202 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7373 (mt0) REVERT: F 151 MET cc_start: 0.6681 (mmp) cc_final: 0.6469 (mmp) REVERT: F 302 GLU cc_start: 0.7202 (tt0) cc_final: 0.6943 (tm-30) outliers start: 13 outliers final: 5 residues processed: 453 average time/residue: 0.1378 time to fit residues: 89.4167 Evaluate side-chains 453 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 447 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain E residue 13 ASP Chi-restraints excluded: chain E residue 202 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 227 ASN B 279 ASN B 296 ASN D 227 ASN F 64 ASN F 96 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.148906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.123210 restraints weight = 25722.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.127550 restraints weight = 12956.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.130524 restraints weight = 7904.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132487 restraints weight = 5464.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133515 restraints weight = 4154.451| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17264 Z= 0.142 Angle : 0.509 9.302 23476 Z= 0.268 Chirality : 0.041 0.128 2657 Planarity : 0.004 0.055 3058 Dihedral : 7.545 157.864 2421 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.21 % Allowed : 32.37 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.18), residues: 2103 helix: 0.21 (0.17), residues: 918 sheet: -0.67 (0.27), residues: 331 loop : -0.95 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 51 TYR 0.010 0.001 TYR D 132 PHE 0.011 0.001 PHE F 61 TRP 0.008 0.001 TRP D 130 HIS 0.007 0.001 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (17264) covalent geometry : angle 0.50884 / 0.27 (23476) hydrogen bonds : bond 0.03607 / 2.46 ( 722) hydrogen bonds : angle 5.03402 / 3.52 ( 2043) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 472 time to evaluate : 0.607 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: A 64 ASN cc_start: 0.7318 (t0) cc_final: 0.7064 (t0) REVERT: A 94 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7190 (ttp-110) REVERT: A 217 LEU cc_start: 0.6868 (tp) cc_final: 0.6659 (tt) REVERT: A 278 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6337 (pm20) REVERT: C 61 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.7043 (t80) REVERT: C 248 MET cc_start: 0.7137 (mmt) cc_final: 0.6763 (mmt) REVERT: C 261 ASN cc_start: 0.6868 (m-40) cc_final: 0.6623 (m110) REVERT: C 296 ASN cc_start: 0.8559 (m-40) cc_final: 0.8309 (m110) REVERT: D 227 ASN cc_start: 0.8266 (m110) cc_final: 0.7740 (m-40) REVERT: D 254 MET cc_start: 0.7373 (mtm) cc_final: 0.6987 (mtm) REVERT: E 94 ARG cc_start: 0.7205 (mtp-110) cc_final: 0.6993 (mtp-110) REVERT: F 151 MET cc_start: 0.6701 (mmp) cc_final: 0.6299 (mmt) REVERT: G 382 GLU cc_start: 0.6547 (mm-30) cc_final: 0.6083 (tm-30) REVERT: G 512 GLU cc_start: 0.3633 (OUTLIER) cc_final: 0.3209 (tm-30) REVERT: G 542 MET cc_start: 0.7480 (ttp) cc_final: 0.6991 (ttp) REVERT: G 613 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8178 (tm-30) outliers start: 76 outliers final: 44 residues processed: 518 average time/residue: 0.1327 time to fit residues: 99.2522 Evaluate side-chains 519 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 470 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 169 GLN Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 438 CYS Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 526 TRP Chi-restraints excluded: chain G residue 541 LEU Chi-restraints excluded: chain G residue 594 TYR Chi-restraints excluded: chain G residue 613 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 200 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 37 optimal weight: 0.0050 chunk 171 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 186 ASN B 227 ASN B 279 ASN C 80 HIS C 222 HIS F 96 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.147900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.121288 restraints weight = 25938.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125818 restraints weight = 13010.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.128857 restraints weight = 7929.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.130950 restraints weight = 5532.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.132172 restraints weight = 4197.492| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17264 Z= 0.121 Angle : 0.479 8.192 23476 Z= 0.252 Chirality : 0.041 0.130 2657 Planarity : 0.004 0.050 3058 Dihedral : 6.529 162.484 2409 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.20 % Allowed : 31.93 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.18), residues: 2103 helix: 0.29 (0.17), residues: 912 sheet: -0.62 (0.28), residues: 334 loop : -0.94 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 51 TYR 0.009 0.001 TYR D 219 PHE 0.010 0.001 PHE B 179 TRP 0.010 0.001 TRP C 90 HIS 0.008 0.001 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (17264) covalent geometry : angle 0.47859 / 0.25 (23476) hydrogen bonds : bond 0.03306 / 2.27 ( 722) hydrogen bonds : angle 4.83891 / 3.39 ( 2043) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 462 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7364 (t0) cc_final: 0.7072 (t0) REVERT: A 94 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7173 (ttp-110) REVERT: A 217 LEU cc_start: 0.6858 (tp) cc_final: 0.6650 (tt) REVERT: A 278 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.6332 (pm20) REVERT: B 96 ASN cc_start: 0.7793 (t0) cc_final: 0.7543 (t0) REVERT: C 61 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6985 (t80) REVERT: C 257 GLN cc_start: 0.7510 (tm-30) cc_final: 0.7024 (tm-30) REVERT: C 261 ASN cc_start: 0.6818 (m-40) cc_final: 0.6377 (m110) REVERT: C 291 ARG cc_start: 0.7306 (mtp85) cc_final: 0.7070 (mtp85) REVERT: C 296 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8321 (m110) REVERT: D 227 ASN cc_start: 0.8278 (m110) cc_final: 0.7996 (m-40) REVERT: D 254 MET cc_start: 0.7414 (mtm) cc_final: 0.7006 (mtm) REVERT: E 94 ARG cc_start: 0.7169 (mtp-110) cc_final: 0.6864 (mtp-110) REVERT: F 151 MET cc_start: 0.6754 (mmp) cc_final: 0.6388 (mmt) REVERT: F 208 MET cc_start: 0.7000 (tmm) cc_final: 0.6372 (tmm) REVERT: F 302 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6980 (tm-30) REVERT: G 368 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7091 (ttp-170) REVERT: G 382 GLU cc_start: 0.6550 (mm-30) cc_final: 0.6039 (tm-30) REVERT: G 390 ARG cc_start: 0.7899 (mtt90) cc_final: 0.7677 (mtp85) REVERT: G 512 GLU cc_start: 0.3641 (OUTLIER) cc_final: 0.3305 (tm-30) REVERT: G 542 MET cc_start: 0.7484 (ttp) cc_final: 0.6852 (ttp) REVERT: G 568 ARG cc_start: 0.7807 (mmt90) cc_final: 0.7443 (mmp80) outliers start: 94 outliers final: 57 residues processed: 527 average time/residue: 0.1311 time to fit residues: 99.5293 Evaluate side-chains 519 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 456 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 253 ASP Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 368 ARG Chi-restraints excluded: chain G residue 409 ASP Chi-restraints excluded: chain G residue 438 CYS Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 526 TRP Chi-restraints excluded: chain G residue 541 LEU Chi-restraints excluded: chain G residue 594 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 43 optimal weight: 0.2980 chunk 75 optimal weight: 0.9980 chunk 1 optimal weight: 0.0170 chunk 42 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 181 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 227 ASN C 80 HIS C 224 ASN E 10 ASN F 96 ASN ** F 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.149816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.123108 restraints weight = 25731.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.127648 restraints weight = 12972.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130670 restraints weight = 7951.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.132717 restraints weight = 5566.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.134097 restraints weight = 4257.082| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17264 Z= 0.111 Angle : 0.469 7.861 23476 Z= 0.247 Chirality : 0.040 0.129 2657 Planarity : 0.004 0.048 3058 Dihedral : 6.467 162.985 2409 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 5.15 % Allowed : 32.48 % Favored : 62.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.18), residues: 2103 helix: 0.37 (0.17), residues: 911 sheet: -0.59 (0.27), residues: 338 loop : -0.93 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 51 TYR 0.015 0.001 TYR D 219 PHE 0.009 0.001 PHE B 179 TRP 0.009 0.001 TRP E 211 HIS 0.008 0.001 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (17264) covalent geometry : angle 0.46892 / 0.25 (23476) hydrogen bonds : bond 0.03149 / 2.17 ( 722) hydrogen bonds : angle 4.74023 / 3.32 ( 2043) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 458 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7403 (t0) cc_final: 0.7082 (t0) REVERT: A 94 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.7141 (ttp-110) REVERT: A 217 LEU cc_start: 0.6836 (tp) cc_final: 0.6624 (tt) REVERT: A 278 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6315 (pm20) REVERT: B 11 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7973 (tt) REVERT: B 96 ASN cc_start: 0.7747 (t0) cc_final: 0.6807 (t0) REVERT: B 98 ASP cc_start: 0.5948 (p0) cc_final: 0.5665 (p0) REVERT: B 279 ASN cc_start: 0.7783 (m-40) cc_final: 0.7577 (m110) REVERT: C 61 PHE cc_start: 0.7351 (OUTLIER) cc_final: 0.6999 (t80) REVERT: C 250 ARG cc_start: 0.7810 (mmt180) cc_final: 0.7370 (mmp-170) REVERT: C 261 ASN cc_start: 0.6771 (m-40) cc_final: 0.6371 (m110) REVERT: C 291 ARG cc_start: 0.7307 (mtp85) cc_final: 0.7066 (mtp85) REVERT: C 296 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8287 (m110) REVERT: D 122 GLU cc_start: 0.7116 (pt0) cc_final: 0.6703 (pt0) REVERT: D 211 TRP cc_start: 0.8223 (m100) cc_final: 0.6557 (m100) REVERT: D 227 ASN cc_start: 0.8321 (m110) cc_final: 0.7922 (m110) REVERT: D 254 MET cc_start: 0.7405 (mtm) cc_final: 0.7069 (mtm) REVERT: E 94 ARG cc_start: 0.7202 (mtp-110) cc_final: 0.6909 (mtp-110) REVERT: F 208 MET cc_start: 0.6997 (tmm) cc_final: 0.6527 (tmm) REVERT: F 302 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6949 (tm-30) REVERT: G 366 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7108 (tp40) REVERT: G 368 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7079 (ttp-170) REVERT: G 512 GLU cc_start: 0.3612 (OUTLIER) cc_final: 0.3287 (tm-30) REVERT: G 542 MET cc_start: 0.7532 (ttp) cc_final: 0.6895 (ttp) REVERT: G 568 ARG cc_start: 0.7829 (mmt90) cc_final: 0.7509 (mmp80) REVERT: G 613 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8215 (tm-30) outliers start: 93 outliers final: 57 residues processed: 522 average time/residue: 0.1245 time to fit residues: 94.4055 Evaluate side-chains 519 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 453 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain G residue 368 ARG Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 438 CYS Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 541 LEU Chi-restraints excluded: chain G residue 594 TYR Chi-restraints excluded: chain G residue 613 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 58 optimal weight: 6.9990 chunk 25 optimal weight: 0.1980 chunk 204 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 53 optimal weight: 0.0870 chunk 145 optimal weight: 0.0020 chunk 94 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 126 optimal weight: 2.9990 overall best weight: 0.2366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 80 HIS B 186 ASN B 227 ASN C 80 HIS E 10 ASN F 96 ASN F 235 HIS ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.151843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125135 restraints weight = 25689.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.129723 restraints weight = 12909.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.132839 restraints weight = 7873.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134924 restraints weight = 5463.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136107 restraints weight = 4151.446| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17264 Z= 0.086 Angle : 0.457 8.828 23476 Z= 0.239 Chirality : 0.040 0.131 2657 Planarity : 0.004 0.049 3058 Dihedral : 6.338 164.496 2409 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 5.31 % Allowed : 32.15 % Favored : 62.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 2103 helix: 0.49 (0.18), residues: 907 sheet: -0.56 (0.27), residues: 345 loop : -0.89 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 51 TYR 0.011 0.001 TYR C 310 PHE 0.011 0.001 PHE D 314 TRP 0.009 0.001 TRP F 90 HIS 0.008 0.001 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.09 (17264) covalent geometry : angle 0.45712 / 0.24 (23476) hydrogen bonds : bond 0.02763 / 1.89 ( 722) hydrogen bonds : angle 4.57356 / 3.22 ( 2043) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 449 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7115 (ttp-110) REVERT: A 217 LEU cc_start: 0.6823 (tp) cc_final: 0.6617 (tt) REVERT: A 242 ARG cc_start: 0.7541 (ptm-80) cc_final: 0.6888 (ptm-80) REVERT: A 278 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.6302 (pm20) REVERT: B 135 ASN cc_start: 0.7498 (p0) cc_final: 0.7238 (p0) REVERT: C 61 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.6949 (t80) REVERT: C 250 ARG cc_start: 0.7723 (mmt180) cc_final: 0.7437 (mmp80) REVERT: C 257 GLN cc_start: 0.7417 (tm-30) cc_final: 0.6927 (tm-30) REVERT: C 261 ASN cc_start: 0.6685 (m-40) cc_final: 0.6239 (m110) REVERT: C 291 ARG cc_start: 0.7280 (mtp85) cc_final: 0.7062 (mtp85) REVERT: C 296 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8245 (m110) REVERT: D 122 GLU cc_start: 0.7124 (pt0) cc_final: 0.6702 (pt0) REVERT: D 202 GLN cc_start: 0.5980 (OUTLIER) cc_final: 0.5688 (pp30) REVERT: D 211 TRP cc_start: 0.8147 (m100) cc_final: 0.6287 (m100) REVERT: D 227 ASN cc_start: 0.8289 (m110) cc_final: 0.7824 (m-40) REVERT: D 251 VAL cc_start: 0.7809 (OUTLIER) cc_final: 0.7325 (p) REVERT: D 254 MET cc_start: 0.7379 (mtm) cc_final: 0.7082 (mtm) REVERT: D 272 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8026 (p) REVERT: E 309 PHE cc_start: 0.7922 (m-10) cc_final: 0.7717 (m-10) REVERT: F 80 HIS cc_start: 0.7142 (OUTLIER) cc_final: 0.6898 (m-70) REVERT: F 96 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.6393 (t0) REVERT: F 101 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7891 (t) REVERT: F 142 GLU cc_start: 0.7143 (mp0) cc_final: 0.6728 (mp0) REVERT: F 151 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6284 (mpp) REVERT: F 208 MET cc_start: 0.6979 (tmm) cc_final: 0.6518 (tmm) REVERT: F 292 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7457 (mp) REVERT: F 302 GLU cc_start: 0.7394 (tm-30) cc_final: 0.6906 (tm-30) REVERT: G 366 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.6860 (tp40) REVERT: G 368 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7037 (ttp-170) REVERT: G 512 GLU cc_start: 0.3867 (OUTLIER) cc_final: 0.3494 (tm-30) REVERT: G 542 MET cc_start: 0.7562 (ttp) cc_final: 0.6930 (ttp) REVERT: G 568 ARG cc_start: 0.7855 (mmt90) cc_final: 0.7578 (mmp80) outliers start: 96 outliers final: 54 residues processed: 512 average time/residue: 0.1381 time to fit residues: 102.1203 Evaluate side-chains 517 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 448 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain G residue 368 ARG Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 409 ASP Chi-restraints excluded: chain G residue 438 CYS Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 541 LEU Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 594 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 126 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 58 optimal weight: 0.0040 chunk 67 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 203 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN B 227 ASN C 133 GLN E 10 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.150460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123698 restraints weight = 25649.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.128239 restraints weight = 12943.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.131235 restraints weight = 7943.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.133279 restraints weight = 5572.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.134477 restraints weight = 4270.384| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17264 Z= 0.122 Angle : 0.485 8.569 23476 Z= 0.251 Chirality : 0.041 0.124 2657 Planarity : 0.004 0.048 3058 Dihedral : 6.392 163.192 2409 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.93 % Allowed : 32.54 % Favored : 62.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.18), residues: 2103 helix: 0.47 (0.18), residues: 907 sheet: -0.51 (0.27), residues: 347 loop : -0.86 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 51 TYR 0.013 0.001 TYR E 63 PHE 0.009 0.001 PHE B 179 TRP 0.008 0.001 TRP E 211 HIS 0.007 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (17264) covalent geometry : angle 0.48467 / 0.25 (23476) hydrogen bonds : bond 0.03082 / 2.14 ( 722) hydrogen bonds : angle 4.63169 / 3.26 ( 2043) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 463 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7159 (ttp-110) REVERT: A 217 LEU cc_start: 0.6841 (tp) cc_final: 0.6634 (tt) REVERT: A 242 ARG cc_start: 0.7558 (ptm-80) cc_final: 0.7204 (ptm-80) REVERT: A 278 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6319 (pm20) REVERT: B 33 TYR cc_start: 0.8028 (m-80) cc_final: 0.7230 (m-80) REVERT: C 61 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.7029 (t80) REVERT: C 214 VAL cc_start: 0.8082 (t) cc_final: 0.7694 (p) REVERT: C 248 MET cc_start: 0.7005 (mmt) cc_final: 0.6621 (mmt) REVERT: C 257 GLN cc_start: 0.7459 (tm-30) cc_final: 0.6988 (tm-30) REVERT: C 261 ASN cc_start: 0.6738 (m-40) cc_final: 0.6225 (m110) REVERT: D 122 GLU cc_start: 0.7103 (pt0) cc_final: 0.6696 (pt0) REVERT: D 227 ASN cc_start: 0.8317 (m110) cc_final: 0.7779 (m110) REVERT: D 251 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7424 (p) REVERT: D 254 MET cc_start: 0.7384 (mtm) cc_final: 0.7052 (mtm) REVERT: E 94 ARG cc_start: 0.7310 (mtp-110) cc_final: 0.7002 (mtp-110) REVERT: F 101 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.7968 (t) REVERT: F 151 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6275 (mpp) REVERT: F 208 MET cc_start: 0.6986 (tmm) cc_final: 0.6647 (tmm) REVERT: F 302 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6897 (tm-30) REVERT: G 366 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.6861 (tp40) REVERT: G 368 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7095 (ttp-170) REVERT: G 454 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6859 (mm-30) REVERT: G 512 GLU cc_start: 0.3865 (OUTLIER) cc_final: 0.3486 (tm-30) REVERT: G 538 ARG cc_start: 0.7355 (ttm110) cc_final: 0.7076 (ttm110) REVERT: G 542 MET cc_start: 0.7585 (ttp) cc_final: 0.6959 (ttp) REVERT: G 568 ARG cc_start: 0.7853 (mmt90) cc_final: 0.7589 (mmp80) REVERT: G 613 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8200 (tm-30) outliers start: 89 outliers final: 65 residues processed: 519 average time/residue: 0.1387 time to fit residues: 104.6012 Evaluate side-chains 533 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 458 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain G residue 368 ARG Chi-restraints excluded: chain G residue 438 CYS Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 541 LEU Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 594 TYR Chi-restraints excluded: chain G residue 613 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 29 optimal weight: 0.0970 chunk 104 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.0070 chunk 44 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 227 ASN C 224 ASN D 227 ASN E 10 ASN F 96 ASN F 227 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.148668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121941 restraints weight = 25575.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.126423 restraints weight = 12957.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.129444 restraints weight = 7970.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.131285 restraints weight = 5583.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.132714 restraints weight = 4348.014| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17264 Z= 0.160 Angle : 0.512 8.079 23476 Z= 0.268 Chirality : 0.042 0.156 2657 Planarity : 0.004 0.049 3058 Dihedral : 6.512 161.844 2409 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.26 % Allowed : 32.82 % Favored : 61.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.18), residues: 2103 helix: 0.38 (0.17), residues: 905 sheet: -0.39 (0.28), residues: 325 loop : -0.89 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 51 TYR 0.013 0.001 TYR E 63 PHE 0.011 0.001 PHE F 283 TRP 0.022 0.001 TRP E 211 HIS 0.008 0.001 HIS F 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (17264) covalent geometry : angle 0.51200 / 0.27 (23476) hydrogen bonds : bond 0.03474 / 2.40 ( 722) hydrogen bonds : angle 4.73450 / 3.33 ( 2043) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 477 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7160 (ttp-110) REVERT: A 97 LEU cc_start: 0.8071 (mm) cc_final: 0.7830 (mt) REVERT: A 217 LEU cc_start: 0.6872 (tp) cc_final: 0.6657 (tt) REVERT: A 278 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.6327 (pm20) REVERT: B 282 ILE cc_start: 0.8125 (tt) cc_final: 0.7891 (tt) REVERT: C 61 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.7075 (t80) REVERT: C 214 VAL cc_start: 0.8129 (t) cc_final: 0.7719 (p) REVERT: C 248 MET cc_start: 0.7114 (mmt) cc_final: 0.6861 (mmt) REVERT: C 257 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7096 (tm-30) REVERT: C 261 ASN cc_start: 0.6831 (m-40) cc_final: 0.6271 (m110) REVERT: C 291 ARG cc_start: 0.7368 (mtp85) cc_final: 0.6981 (mtp85) REVERT: C 296 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8280 (m110) REVERT: D 122 GLU cc_start: 0.7085 (pt0) cc_final: 0.6693 (pt0) REVERT: D 136 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8258 (m) REVERT: D 227 ASN cc_start: 0.8410 (m-40) cc_final: 0.7776 (m110) REVERT: D 254 MET cc_start: 0.7387 (mtm) cc_final: 0.7088 (mtm) REVERT: E 94 ARG cc_start: 0.7284 (mtp-110) cc_final: 0.7046 (mtp-110) REVERT: E 253 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6743 (t0) REVERT: E 254 MET cc_start: 0.7176 (ttt) cc_final: 0.6918 (ttt) REVERT: E 309 PHE cc_start: 0.8038 (m-10) cc_final: 0.7797 (m-10) REVERT: F 151 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6279 (mpp) REVERT: F 208 MET cc_start: 0.6966 (tmm) cc_final: 0.6709 (tmm) REVERT: F 302 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6915 (tm-30) REVERT: G 366 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.6913 (tp40) REVERT: G 368 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7112 (ttp-170) REVERT: G 512 GLU cc_start: 0.3825 (OUTLIER) cc_final: 0.3440 (tm-30) REVERT: G 542 MET cc_start: 0.7590 (ttp) cc_final: 0.6956 (ttp) REVERT: G 568 ARG cc_start: 0.7863 (mmt90) cc_final: 0.7610 (mmp80) REVERT: G 613 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8217 (tm-30) outliers start: 95 outliers final: 66 residues processed: 536 average time/residue: 0.1389 time to fit residues: 108.4081 Evaluate side-chains 549 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 472 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 253 ASP Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain G residue 368 ARG Chi-restraints excluded: chain G residue 438 CYS Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 594 TYR Chi-restraints excluded: chain G residue 613 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 175 optimal weight: 0.6980 chunk 200 optimal weight: 0.7980 chunk 143 optimal weight: 0.1980 chunk 182 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 186 ASN B 227 ASN C 133 GLN E 10 ASN F 96 ASN F 227 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.148797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.122034 restraints weight = 25714.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.126510 restraints weight = 12973.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129497 restraints weight = 7965.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131557 restraints weight = 5590.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.132894 restraints weight = 4273.279| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17264 Z= 0.158 Angle : 0.520 8.807 23476 Z= 0.272 Chirality : 0.042 0.201 2657 Planarity : 0.004 0.050 3058 Dihedral : 6.542 160.721 2409 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.09 % Allowed : 33.37 % Favored : 61.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.18), residues: 2103 helix: 0.33 (0.17), residues: 905 sheet: -0.43 (0.28), residues: 315 loop : -0.88 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 51 TYR 0.019 0.001 TYR E 63 PHE 0.012 0.001 PHE F 283 TRP 0.017 0.001 TRP E 211 HIS 0.011 0.001 HIS F 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (17264) covalent geometry : angle 0.51982 / 0.27 (23476) hydrogen bonds : bond 0.03471 / 2.41 ( 722) hydrogen bonds : angle 4.75578 / 3.35 ( 2043) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 468 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7167 (ttp-110) REVERT: A 97 LEU cc_start: 0.8115 (mm) cc_final: 0.7872 (mt) REVERT: A 217 LEU cc_start: 0.6874 (tp) cc_final: 0.6648 (tt) REVERT: A 278 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.6332 (pm20) REVERT: B 282 ILE cc_start: 0.8145 (tt) cc_final: 0.7928 (tt) REVERT: C 61 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.7083 (t80) REVERT: C 250 ARG cc_start: 0.7840 (mmt180) cc_final: 0.7484 (mmp80) REVERT: C 261 ASN cc_start: 0.6864 (m-40) cc_final: 0.6431 (m110) REVERT: C 291 ARG cc_start: 0.7370 (mtp85) cc_final: 0.6957 (mtp85) REVERT: C 296 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8285 (m110) REVERT: D 122 GLU cc_start: 0.7099 (pt0) cc_final: 0.6713 (pt0) REVERT: D 136 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8258 (m) REVERT: D 227 ASN cc_start: 0.8480 (m-40) cc_final: 0.7887 (m-40) REVERT: D 254 MET cc_start: 0.7417 (mtm) cc_final: 0.7063 (mtm) REVERT: E 94 ARG cc_start: 0.7245 (mtp-110) cc_final: 0.6998 (mtp-110) REVERT: F 101 VAL cc_start: 0.8245 (OUTLIER) cc_final: 0.7954 (t) REVERT: F 151 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6219 (mpp) REVERT: F 208 MET cc_start: 0.6981 (tmm) cc_final: 0.6772 (tmm) REVERT: F 302 GLU cc_start: 0.7330 (tm-30) cc_final: 0.6961 (tm-30) REVERT: G 366 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.6875 (tp40) REVERT: G 368 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7117 (ttp-170) REVERT: G 512 GLU cc_start: 0.3819 (OUTLIER) cc_final: 0.3429 (tm-30) REVERT: G 542 MET cc_start: 0.7608 (ttp) cc_final: 0.6965 (ttp) REVERT: G 568 ARG cc_start: 0.7860 (mmt90) cc_final: 0.7589 (mmp80) outliers start: 92 outliers final: 74 residues processed: 529 average time/residue: 0.1315 time to fit residues: 101.5981 Evaluate side-chains 546 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 462 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 235 HIS Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain G residue 368 ARG Chi-restraints excluded: chain G residue 409 ASP Chi-restraints excluded: chain G residue 438 CYS Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 594 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 13 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 1 optimal weight: 0.0870 chunk 148 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 10 ASN F 227 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.149966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.124105 restraints weight = 25591.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128420 restraints weight = 12944.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131353 restraints weight = 7910.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.133307 restraints weight = 5497.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.134466 restraints weight = 4205.076| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17264 Z= 0.122 Angle : 0.512 9.797 23476 Z= 0.267 Chirality : 0.042 0.238 2657 Planarity : 0.004 0.050 3058 Dihedral : 6.487 160.707 2409 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.98 % Allowed : 33.48 % Favored : 61.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.18), residues: 2103 helix: 0.38 (0.17), residues: 905 sheet: -0.54 (0.29), residues: 320 loop : -0.81 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 51 TYR 0.016 0.001 TYR E 63 PHE 0.009 0.001 PHE B 179 TRP 0.013 0.001 TRP E 211 HIS 0.012 0.001 HIS F 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (17264) covalent geometry : angle 0.51236 / 0.27 (23476) hydrogen bonds : bond 0.03222 / 2.23 ( 722) hydrogen bonds : angle 4.69837 / 3.31 ( 2043) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 462 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7129 (ttp-110) REVERT: A 97 LEU cc_start: 0.8057 (mm) cc_final: 0.7817 (mt) REVERT: A 217 LEU cc_start: 0.6835 (tp) cc_final: 0.6622 (tt) REVERT: A 278 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.6314 (pm20) REVERT: B 282 ILE cc_start: 0.8084 (tt) cc_final: 0.7866 (tt) REVERT: C 61 PHE cc_start: 0.7342 (OUTLIER) cc_final: 0.7026 (t80) REVERT: C 142 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6876 (mt-10) REVERT: C 261 ASN cc_start: 0.6808 (m-40) cc_final: 0.6525 (m110) REVERT: C 291 ARG cc_start: 0.7283 (mtp85) cc_final: 0.6892 (mtp85) REVERT: C 296 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.8250 (m110) REVERT: D 122 GLU cc_start: 0.7086 (pt0) cc_final: 0.6712 (pt0) REVERT: D 211 TRP cc_start: 0.8220 (m100) cc_final: 0.6696 (m100) REVERT: D 227 ASN cc_start: 0.8434 (m-40) cc_final: 0.7810 (m-40) REVERT: D 251 VAL cc_start: 0.7921 (OUTLIER) cc_final: 0.7451 (p) REVERT: D 254 MET cc_start: 0.7365 (mtm) cc_final: 0.7059 (mtm) REVERT: E 94 ARG cc_start: 0.7255 (mtp-110) cc_final: 0.7024 (mtp-110) REVERT: E 314 PHE cc_start: 0.8471 (m-80) cc_final: 0.8140 (m-80) REVERT: F 101 VAL cc_start: 0.8245 (OUTLIER) cc_final: 0.7958 (t) REVERT: F 141 ASP cc_start: 0.7266 (m-30) cc_final: 0.7014 (m-30) REVERT: F 151 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6212 (mpp) REVERT: F 302 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6981 (tm-30) REVERT: G 366 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.6892 (tp40) REVERT: G 368 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7056 (ttp-170) REVERT: G 375 ARG cc_start: 0.7556 (mtt-85) cc_final: 0.7356 (mtt-85) REVERT: G 512 GLU cc_start: 0.3779 (OUTLIER) cc_final: 0.3383 (tm-30) REVERT: G 542 MET cc_start: 0.7580 (ttp) cc_final: 0.6963 (ttp) REVERT: G 568 ARG cc_start: 0.7807 (mmt90) cc_final: 0.7569 (mmp80) outliers start: 90 outliers final: 71 residues processed: 521 average time/residue: 0.1322 time to fit residues: 99.9270 Evaluate side-chains 538 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 457 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 235 HIS Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain G residue 368 ARG Chi-restraints excluded: chain G residue 409 ASP Chi-restraints excluded: chain G residue 438 CYS Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 594 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 24 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 201 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN B 227 ASN C 80 HIS E 10 ASN F 227 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.146181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.119443 restraints weight = 25640.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123929 restraints weight = 13021.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.126912 restraints weight = 7992.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128917 restraints weight = 5598.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.130317 restraints weight = 4306.398| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17264 Z= 0.168 Angle : 0.552 12.945 23476 Z= 0.286 Chirality : 0.043 0.267 2657 Planarity : 0.004 0.050 3058 Dihedral : 6.582 159.709 2409 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.81 % Allowed : 33.81 % Favored : 61.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.18), residues: 2103 helix: 0.26 (0.17), residues: 912 sheet: -0.56 (0.29), residues: 310 loop : -0.90 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 51 TYR 0.015 0.001 TYR E 63 PHE 0.022 0.001 PHE D 314 TRP 0.018 0.001 TRP F 90 HIS 0.013 0.001 HIS F 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (17264) covalent geometry : angle 0.55247 / 0.29 (23476) hydrogen bonds : bond 0.03607 / 2.51 ( 722) hydrogen bonds : angle 4.79980 / 3.37 ( 2043) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 464 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7185 (ttp-110) REVERT: A 97 LEU cc_start: 0.8130 (mm) cc_final: 0.7884 (mt) REVERT: A 211 TRP cc_start: 0.8472 (m100) cc_final: 0.8177 (m100) REVERT: A 278 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.6279 (pm20) REVERT: B 124 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7365 (pttp) REVERT: B 282 ILE cc_start: 0.8153 (tt) cc_final: 0.7949 (tt) REVERT: C 61 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.7131 (t80) REVERT: C 142 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6903 (mt-10) REVERT: C 250 ARG cc_start: 0.7857 (mmt180) cc_final: 0.7538 (mmp80) REVERT: C 261 ASN cc_start: 0.6856 (m-40) cc_final: 0.6569 (m110) REVERT: C 291 ARG cc_start: 0.7316 (mtp85) cc_final: 0.7070 (mtp85) REVERT: C 296 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8311 (m110) REVERT: D 107 VAL cc_start: 0.7951 (m) cc_final: 0.7583 (t) REVERT: D 122 GLU cc_start: 0.7073 (pt0) cc_final: 0.6696 (pt0) REVERT: D 136 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8249 (m) REVERT: D 227 ASN cc_start: 0.8458 (m-40) cc_final: 0.7595 (m-40) REVERT: D 254 MET cc_start: 0.7398 (mtm) cc_final: 0.7028 (mtm) REVERT: D 291 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7610 (ttp80) REVERT: E 94 ARG cc_start: 0.7242 (mtp-110) cc_final: 0.7012 (mtp-110) REVERT: E 314 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8159 (m-80) REVERT: F 141 ASP cc_start: 0.7227 (m-30) cc_final: 0.7025 (m-30) REVERT: F 151 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6271 (mpp) REVERT: F 285 ASP cc_start: 0.7014 (t0) cc_final: 0.6725 (t0) REVERT: F 302 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6980 (tm-30) REVERT: G 366 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.6936 (tp40) REVERT: G 368 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7101 (ttp-170) REVERT: G 375 ARG cc_start: 0.7561 (mtt-85) cc_final: 0.7355 (mtt-85) REVERT: G 512 GLU cc_start: 0.3795 (OUTLIER) cc_final: 0.3402 (tm-30) REVERT: G 542 MET cc_start: 0.7616 (ttp) cc_final: 0.6948 (ttp) REVERT: G 568 ARG cc_start: 0.7821 (mmt90) cc_final: 0.7607 (mmp80) outliers start: 87 outliers final: 71 residues processed: 522 average time/residue: 0.1268 time to fit residues: 95.9581 Evaluate side-chains 544 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 462 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 235 HIS Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 314 PHE Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 366 GLN Chi-restraints excluded: chain G residue 368 ARG Chi-restraints excluded: chain G residue 409 ASP Chi-restraints excluded: chain G residue 438 CYS Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 551 ASP Chi-restraints excluded: chain G residue 594 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 172 optimal weight: 0.7980 chunk 204 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 0.0040 chunk 1 optimal weight: 0.0000 chunk 59 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 119 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 80 HIS E 10 ASN F 96 ASN F 227 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.150784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.123916 restraints weight = 25491.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.128378 restraints weight = 12890.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.131398 restraints weight = 7941.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.133463 restraints weight = 5571.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.134706 restraints weight = 4269.789| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17264 Z= 0.108 Angle : 0.529 12.158 23476 Z= 0.272 Chirality : 0.042 0.242 2657 Planarity : 0.004 0.048 3058 Dihedral : 6.451 159.586 2409 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.26 % Allowed : 34.86 % Favored : 60.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.18), residues: 2103 helix: 0.33 (0.17), residues: 906 sheet: -0.53 (0.28), residues: 322 loop : -0.85 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 51 TYR 0.014 0.001 TYR C 310 PHE 0.009 0.001 PHE B 179 TRP 0.013 0.001 TRP E 211 HIS 0.009 0.001 HIS F 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (17264) covalent geometry : angle 0.52857 / 0.27 (23476) hydrogen bonds : bond 0.03094 / 2.15 ( 722) hydrogen bonds : angle 4.69180 / 3.30 ( 2043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2976.47 seconds wall clock time: 51 minutes 47.62 seconds (3107.62 seconds total)