Starting phenix.real_space_refine on Tue Jun 24 22:54:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ets_28597/06_2025/8ets_28597.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ets_28597/06_2025/8ets_28597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ets_28597/06_2025/8ets_28597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ets_28597/06_2025/8ets_28597.map" model { file = "/net/cci-nas-00/data/ceres_data/8ets_28597/06_2025/8ets_28597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ets_28597/06_2025/8ets_28597.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 95 5.16 5 C 18041 2.51 5 N 4942 2.21 5 O 5580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28670 Number of models: 1 Model: "" Number of chains: 16 Chain: "Q" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3385 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 22, 'TRANS': 395} Chain breaks: 5 Chain: "R" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3548 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain breaks: 1 Chain: "S" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1014 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 9, 'TRANS': 115} Chain breaks: 1 Chain: "T" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3339 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3354 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3404 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 18, 'TRANS': 424} Chain: "W" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3398 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 431} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "Y" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3421 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 434} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 248 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.32, per 1000 atoms: 0.64 Number of scatterers: 28670 At special positions: 0 Unit cell: (161.155, 150.3, 177.855, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 95 16.00 P 12 15.00 O 5580 8.00 N 4942 7.00 C 18041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.59 Conformation dependent library (CDL) restraints added in 3.7 seconds 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6820 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 31 sheets defined 43.7% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'Q' and resid 957 through 971 removed outlier: 3.703A pdb=" N ILE Q 971 " --> pdb=" O LEU Q 967 " (cutoff:3.500A) Processing helix chain 'Q' and resid 974 through 985 Processing helix chain 'Q' and resid 1000 through 1013 removed outlier: 4.028A pdb=" N GLN Q1006 " --> pdb=" O ASN Q1002 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE Q1007 " --> pdb=" O ALA Q1003 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1013 through 1018 removed outlier: 4.129A pdb=" N PHE Q1017 " --> pdb=" O HIS Q1013 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1086 through 1094 removed outlier: 3.875A pdb=" N TYR Q1090 " --> pdb=" O PRO Q1086 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1101 through 1111 Processing helix chain 'Q' and resid 1121 through 1133 Processing helix chain 'Q' and resid 1138 through 1144 Processing helix chain 'Q' and resid 1147 through 1154 Processing helix chain 'Q' and resid 1169 through 1178 removed outlier: 3.770A pdb=" N VAL Q1177 " --> pdb=" O GLU Q1173 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR Q1178 " --> pdb=" O LEU Q1174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1185 through 1190 Processing helix chain 'Q' and resid 1192 through 1201 Processing helix chain 'Q' and resid 1202 through 1206 removed outlier: 3.511A pdb=" N CYS Q1205 " --> pdb=" O TYR Q1202 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE Q1206 " --> pdb=" O LEU Q1203 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1202 through 1206' Processing helix chain 'Q' and resid 1226 through 1238 removed outlier: 3.923A pdb=" N THR Q1230 " --> pdb=" O SER Q1226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1239 through 1246 Processing helix chain 'Q' and resid 1250 through 1259 Processing helix chain 'Q' and resid 1264 through 1268 Processing helix chain 'Q' and resid 1280 through 1284 removed outlier: 3.836A pdb=" N SER Q1283 " --> pdb=" O LYS Q1280 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER Q1284 " --> pdb=" O ASN Q1281 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1280 through 1284' Processing helix chain 'Q' and resid 1292 through 1297 Processing helix chain 'Q' and resid 1298 through 1315 removed outlier: 3.919A pdb=" N VAL Q1309 " --> pdb=" O ASP Q1305 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS Q1310 " --> pdb=" O GLU Q1306 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU Q1311 " --> pdb=" O LEU Q1307 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1325 through 1339 Processing helix chain 'Q' and resid 1357 through 1364 Processing helix chain 'Q' and resid 1397 through 1408 removed outlier: 4.327A pdb=" N GLN Q1403 " --> pdb=" O THR Q1399 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA Q1408 " --> pdb=" O ALA Q1404 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1427 through 1432 removed outlier: 3.710A pdb=" N ARG Q1431 " --> pdb=" O THR Q1427 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 34 removed outlier: 3.717A pdb=" N ALA R 33 " --> pdb=" O GLU R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 87 Processing helix chain 'R' and resid 89 through 95 Processing helix chain 'R' and resid 108 through 122 Processing helix chain 'R' and resid 143 through 158 removed outlier: 4.025A pdb=" N ARG R 147 " --> pdb=" O VAL R 143 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU R 156 " --> pdb=" O GLN R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 177 Processing helix chain 'R' and resid 215 through 231 removed outlier: 3.671A pdb=" N TYR R 231 " --> pdb=" O MET R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 250 removed outlier: 3.633A pdb=" N TYR R 243 " --> pdb=" O SER R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 261 Processing helix chain 'R' and resid 585 through 588 removed outlier: 3.794A pdb=" N ASN R 588 " --> pdb=" O ASP R 585 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 585 through 588' Processing helix chain 'R' and resid 589 through 597 Processing helix chain 'R' and resid 607 through 609 No H-bonds generated for 'chain 'R' and resid 607 through 609' Processing helix chain 'R' and resid 616 through 621 Processing helix chain 'R' and resid 622 through 626 removed outlier: 3.979A pdb=" N ILE R 625 " --> pdb=" O PRO R 622 " (cutoff:3.500A) Processing helix chain 'R' and resid 627 through 631 Processing helix chain 'R' and resid 637 through 649 removed outlier: 3.623A pdb=" N LYS R 649 " --> pdb=" O ILE R 645 " (cutoff:3.500A) Processing helix chain 'R' and resid 658 through 666 Processing helix chain 'R' and resid 679 through 692 Processing helix chain 'R' and resid 708 through 720 Processing helix chain 'R' and resid 731 through 738 Processing helix chain 'S' and resid 31 through 40 removed outlier: 4.012A pdb=" N SER S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL S 36 " --> pdb=" O PHE S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 83 removed outlier: 3.563A pdb=" N LEU S 66 " --> pdb=" O SER S 62 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE S 67 " --> pdb=" O ALA S 63 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER S 68 " --> pdb=" O ARG S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 104 removed outlier: 3.763A pdb=" N VAL S 103 " --> pdb=" O THR S 99 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU S 104 " --> pdb=" O TYR S 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 99 through 104' Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'S' and resid 150 through 157 removed outlier: 3.945A pdb=" N GLU S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 68 removed outlier: 3.901A pdb=" N LYS T 68 " --> pdb=" O LEU T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 97 removed outlier: 3.601A pdb=" N GLY T 97 " --> pdb=" O SER T 93 " (cutoff:3.500A) Processing helix chain 'T' and resid 108 through 111 removed outlier: 3.566A pdb=" N TYR T 111 " --> pdb=" O SER T 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 108 through 111' Processing helix chain 'T' and resid 116 through 127 Processing helix chain 'T' and resid 182 through 192 Processing helix chain 'T' and resid 217 through 219 No H-bonds generated for 'chain 'T' and resid 217 through 219' Processing helix chain 'T' and resid 249 through 257 Processing helix chain 'T' and resid 281 through 298 removed outlier: 3.566A pdb=" N ARG T 285 " --> pdb=" O THR T 281 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN T 298 " --> pdb=" O LYS T 294 " (cutoff:3.500A) Processing helix chain 'T' and resid 313 through 316 Processing helix chain 'T' and resid 317 through 328 removed outlier: 3.864A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) Processing helix chain 'T' and resid 360 through 365 removed outlier: 3.811A pdb=" N ASP T 365 " --> pdb=" O PRO T 361 " (cutoff:3.500A) Processing helix chain 'T' and resid 376 through 391 Processing helix chain 'T' and resid 396 through 410 Processing helix chain 'T' and resid 411 through 429 removed outlier: 4.108A pdb=" N ALA T 415 " --> pdb=" O SER T 411 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU T 416 " --> pdb=" O LEU T 412 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA T 420 " --> pdb=" O LEU T 416 " (cutoff:3.500A) Proline residue: T 421 - end of helix removed outlier: 3.538A pdb=" N SER T 429 " --> pdb=" O LEU T 425 " (cutoff:3.500A) Processing helix chain 'T' and resid 435 through 446 Processing helix chain 'T' and resid 448 through 458 Processing helix chain 'U' and resid 47 through 64 removed outlier: 3.508A pdb=" N GLY U 64 " --> pdb=" O MET U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 93 removed outlier: 3.704A pdb=" N GLY U 93 " --> pdb=" O SER U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 123 Processing helix chain 'U' and resid 172 through 181 Processing helix chain 'U' and resid 241 through 249 Processing helix chain 'U' and resid 255 through 260 Processing helix chain 'U' and resid 266 through 284 removed outlier: 4.052A pdb=" N ARG U 270 " --> pdb=" O ARG U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 298 through 301 removed outlier: 3.575A pdb=" N LEU U 301 " --> pdb=" O VAL U 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 298 through 301' Processing helix chain 'U' and resid 302 through 312 removed outlier: 3.572A pdb=" N ARG U 311 " --> pdb=" O SER U 307 " (cutoff:3.500A) Processing helix chain 'U' and resid 340 through 343 Processing helix chain 'U' and resid 344 through 350 removed outlier: 3.808A pdb=" N ARG U 350 " --> pdb=" O ASP U 346 " (cutoff:3.500A) Processing helix chain 'U' and resid 360 through 375 Processing helix chain 'U' and resid 380 through 394 Processing helix chain 'U' and resid 395 through 413 removed outlier: 3.595A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL U 405 " --> pdb=" O ASN U 401 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN U 407 " --> pdb=" O ILE U 403 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE U 409 " --> pdb=" O VAL U 405 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG U 413 " --> pdb=" O ILE U 409 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 removed outlier: 3.527A pdb=" N VAL U 423 " --> pdb=" O GLU U 419 " (cutoff:3.500A) Processing helix chain 'U' and resid 432 through 442 removed outlier: 3.932A pdb=" N GLU U 442 " --> pdb=" O LYS U 438 " (cutoff:3.500A) Processing helix chain 'U' and resid 443 through 447 Processing helix chain 'V' and resid 51 through 68 removed outlier: 3.820A pdb=" N LYS V 68 " --> pdb=" O LEU V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 97 Processing helix chain 'V' and resid 108 through 111 removed outlier: 3.732A pdb=" N TYR V 111 " --> pdb=" O SER V 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 108 through 111' Processing helix chain 'V' and resid 116 through 128 Processing helix chain 'V' and resid 182 through 192 removed outlier: 3.677A pdb=" N TYR V 186 " --> pdb=" O ASP V 182 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER V 188 " --> pdb=" O THR V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 249 through 258 Processing helix chain 'V' and resid 264 through 271 removed outlier: 3.945A pdb=" N GLN V 271 " --> pdb=" O SER V 267 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 298 removed outlier: 3.519A pdb=" N ARG V 285 " --> pdb=" O THR V 281 " (cutoff:3.500A) Processing helix chain 'V' and resid 312 through 316 Processing helix chain 'V' and resid 317 through 328 removed outlier: 3.757A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) Processing helix chain 'V' and resid 360 through 365 removed outlier: 3.564A pdb=" N ASP V 365 " --> pdb=" O PRO V 361 " (cutoff:3.500A) Processing helix chain 'V' and resid 376 through 391 Processing helix chain 'V' and resid 396 through 410 Processing helix chain 'V' and resid 411 through 417 Processing helix chain 'V' and resid 418 through 428 removed outlier: 3.540A pdb=" N CYS V 422 " --> pdb=" O LEU V 418 " (cutoff:3.500A) Processing helix chain 'V' and resid 435 through 446 removed outlier: 3.528A pdb=" N VAL V 439 " --> pdb=" O VAL V 435 " (cutoff:3.500A) Processing helix chain 'V' and resid 448 through 458 Processing helix chain 'W' and resid 47 through 64 removed outlier: 3.604A pdb=" N GLY W 64 " --> pdb=" O MET W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 92 Processing helix chain 'W' and resid 104 through 106 No H-bonds generated for 'chain 'W' and resid 104 through 106' Processing helix chain 'W' and resid 112 through 123 Processing helix chain 'W' and resid 172 through 181 Processing helix chain 'W' and resid 241 through 250 removed outlier: 4.289A pdb=" N ARG W 250 " --> pdb=" O VAL W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 252 through 260 removed outlier: 3.617A pdb=" N ALA W 256 " --> pdb=" O GLN W 252 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE W 258 " --> pdb=" O PHE W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 283 removed outlier: 3.711A pdb=" N ARG W 270 " --> pdb=" O ARG W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 313 removed outlier: 3.798A pdb=" N ARG W 311 " --> pdb=" O SER W 307 " (cutoff:3.500A) Processing helix chain 'W' and resid 340 through 343 Processing helix chain 'W' and resid 344 through 350 removed outlier: 3.784A pdb=" N ARG W 350 " --> pdb=" O ASP W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 375 Processing helix chain 'W' and resid 380 through 394 Processing helix chain 'W' and resid 395 through 411 removed outlier: 3.781A pdb=" N SER W 399 " --> pdb=" O SER W 395 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 430 removed outlier: 3.522A pdb=" N VAL W 423 " --> pdb=" O GLU W 419 " (cutoff:3.500A) Processing helix chain 'W' and resid 432 through 442 removed outlier: 3.648A pdb=" N GLU W 442 " --> pdb=" O LYS W 438 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 67 Processing helix chain 'X' and resid 84 through 97 Processing helix chain 'X' and resid 108 through 111 removed outlier: 3.580A pdb=" N TYR X 111 " --> pdb=" O SER X 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 108 through 111' Processing helix chain 'X' and resid 116 through 127 Processing helix chain 'X' and resid 184 through 192 removed outlier: 4.091A pdb=" N SER X 188 " --> pdb=" O THR X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 219 No H-bonds generated for 'chain 'X' and resid 217 through 219' Processing helix chain 'X' and resid 249 through 258 removed outlier: 3.724A pdb=" N ARG X 258 " --> pdb=" O VAL X 254 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 272 removed outlier: 3.942A pdb=" N MET X 268 " --> pdb=" O ASP X 264 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 298 removed outlier: 3.750A pdb=" N ARG X 285 " --> pdb=" O THR X 281 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN X 298 " --> pdb=" O LYS X 294 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 316 Processing helix chain 'X' and resid 317 through 328 Processing helix chain 'X' and resid 360 through 365 Processing helix chain 'X' and resid 376 through 391 Processing helix chain 'X' and resid 396 through 410 Processing helix chain 'X' and resid 411 through 418 Processing helix chain 'X' and resid 419 through 429 removed outlier: 3.564A pdb=" N SER X 429 " --> pdb=" O LEU X 425 " (cutoff:3.500A) Processing helix chain 'X' and resid 435 through 446 Processing helix chain 'X' and resid 448 through 458 Processing helix chain 'Y' and resid 49 through 64 Processing helix chain 'Y' and resid 80 through 93 removed outlier: 3.868A pdb=" N GLY Y 93 " --> pdb=" O SER Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'Y' and resid 172 through 181 Processing helix chain 'Y' and resid 207 through 209 No H-bonds generated for 'chain 'Y' and resid 207 through 209' Processing helix chain 'Y' and resid 241 through 248 Processing helix chain 'Y' and resid 253 through 260 Processing helix chain 'Y' and resid 266 through 284 removed outlier: 3.737A pdb=" N ARG Y 270 " --> pdb=" O ARG Y 266 " (cutoff:3.500A) Processing helix chain 'Y' and resid 302 through 312 Processing helix chain 'Y' and resid 344 through 350 Processing helix chain 'Y' and resid 360 through 375 Processing helix chain 'Y' and resid 380 through 394 Processing helix chain 'Y' and resid 395 through 413 removed outlier: 3.857A pdb=" N SER Y 399 " --> pdb=" O SER Y 395 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 removed outlier: 3.534A pdb=" N VAL Y 423 " --> pdb=" O GLU Y 419 " (cutoff:3.500A) Processing helix chain 'Y' and resid 432 through 442 Processing helix chain 'Y' and resid 443 through 447 removed outlier: 3.597A pdb=" N TYR Y 447 " --> pdb=" O GLU Y 444 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 949 through 954 removed outlier: 7.219A pdb=" N ILE Q 950 " --> pdb=" O ARG Q1421 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N LEU Q1423 " --> pdb=" O ILE Q 950 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL Q 952 " --> pdb=" O LEU Q1423 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU Q1422 " --> pdb=" O PHE Q1391 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU Q1319 " --> pdb=" O ILE Q1390 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL Q1318 " --> pdb=" O PHE Q1370 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU Q1372 " --> pdb=" O VAL Q1318 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE Q1320 " --> pdb=" O LEU Q1372 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 1026 through 1027 removed outlier: 6.059A pdb=" N PHE Q1026 " --> pdb=" O SER Q1215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'Q' and resid 1071 through 1073 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 1071 through 1073 current: chain 'V' and resid 163 through 172 removed outlier: 3.737A pdb=" N GLY V 175 " --> pdb=" O SER V 172 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 175 through 181 current: chain 'V' and resid 209 through 215 removed outlier: 6.350A pdb=" N VAL V 230 " --> pdb=" O VAL V 212 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG V 214 " --> pdb=" O VAL V 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 1082 through 1084 removed outlier: 6.034A pdb=" N TYR Q1083 " --> pdb=" O GLU Q1222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'R' and resid 14 through 15 Processing sheet with id=AA6, first strand: chain 'R' and resid 61 through 64 removed outlier: 6.732A pdb=" N ILE R 40 " --> pdb=" O LEU R 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 67 through 72 removed outlier: 3.749A pdb=" N LYS R 77 " --> pdb=" O ASP R 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 100 through 101 removed outlier: 3.870A pdb=" N PHE R 104 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 184 through 189 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 203 through 204 current: chain 'R' and resid 700 through 702 Processing sheet with id=AB1, first strand: chain 'S' and resid 125 through 126 removed outlier: 3.501A pdb=" N TYR S 125 " --> pdb=" O TYR S 134 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 102 through 106 removed outlier: 6.336A pdb=" N CYS T 103 " --> pdb=" O PHE T 309 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ASP T 311 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU T 105 " --> pdb=" O ASP T 311 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE T 75 " --> pdb=" O LEU T 338 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N SER T 340 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU T 77 " --> pdb=" O SER T 340 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ALA T 74 " --> pdb=" O LEU T 368 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N VAL T 370 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU T 76 " --> pdb=" O VAL T 370 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N THR T 372 " --> pdb=" O LEU T 76 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA T 78 " --> pdb=" O THR T 372 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 129 through 151 removed outlier: 6.386A pdb=" N GLY T 169 " --> pdb=" O THR T 145 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU T 147 " --> pdb=" O ILE T 167 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE T 167 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS T 165 " --> pdb=" O PRO T 149 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASP T 151 " --> pdb=" O ILE T 163 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE T 163 " --> pdb=" O ASP T 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 175 through 181 current: chain 'T' and resid 209 through 215 removed outlier: 6.469A pdb=" N VAL T 230 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ARG T 214 " --> pdb=" O VAL T 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 344 through 346 Processing sheet with id=AB5, first strand: chain 'U' and resid 40 through 41 Processing sheet with id=AB6, first strand: chain 'U' and resid 98 through 102 removed outlier: 6.285A pdb=" N THR U 99 " --> pdb=" O PHE U 294 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP U 296 " --> pdb=" O THR U 99 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE U 101 " --> pdb=" O ASP U 296 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 125 through 147 removed outlier: 5.361A pdb=" N VAL U 140 " --> pdb=" O LYS U 161 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS U 161 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 166 through 171 current: chain 'U' and resid 199 through 204 Processing sheet with id=AB8, first strand: chain 'U' and resid 330 through 331 Processing sheet with id=AB9, first strand: chain 'V' and resid 44 through 45 removed outlier: 3.599A pdb=" N GLU V 45 " --> pdb=" O PHE V 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'V' and resid 102 through 106 removed outlier: 6.382A pdb=" N CYS V 103 " --> pdb=" O PHE V 309 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASP V 311 " --> pdb=" O CYS V 103 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU V 105 " --> pdb=" O ASP V 311 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU V 308 " --> pdb=" O VAL V 337 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ALA V 339 " --> pdb=" O LEU V 308 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE V 310 " --> pdb=" O ALA V 339 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ALA V 74 " --> pdb=" O LEU V 368 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL V 370 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU V 76 " --> pdb=" O VAL V 370 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'V' and resid 344 through 346 Processing sheet with id=AC3, first strand: chain 'W' and resid 40 through 41 Processing sheet with id=AC4, first strand: chain 'W' and resid 98 through 102 removed outlier: 6.272A pdb=" N THR W 99 " --> pdb=" O PHE W 294 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASP W 296 " --> pdb=" O THR W 99 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE W 101 " --> pdb=" O ASP W 296 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU W 293 " --> pdb=" O MET W 322 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ALA W 324 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE W 295 " --> pdb=" O ALA W 324 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 125 through 147 removed outlier: 5.179A pdb=" N VAL W 140 " --> pdb=" O LYS W 161 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LYS W 161 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU W 142 " --> pdb=" O THR W 159 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 166 through 171 current: chain 'W' and resid 198 through 204 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 198 through 204 current: chain 'X' and resid 160 through 172 removed outlier: 3.554A pdb=" N VAL X 166 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY X 175 " --> pdb=" O SER X 172 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 175 through 181 current: chain 'X' and resid 211 through 215 removed outlier: 6.533A pdb=" N VAL X 230 " --> pdb=" O VAL X 212 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ARG X 214 " --> pdb=" O VAL X 230 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 229 through 230 current: chain 'Z' and resid 315 through 319 Processing sheet with id=AC6, first strand: chain 'W' and resid 330 through 331 Processing sheet with id=AC7, first strand: chain 'X' and resid 44 through 45 removed outlier: 4.052A pdb=" N GLU X 45 " --> pdb=" O PHE X 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 102 through 106 removed outlier: 6.383A pdb=" N ILE X 75 " --> pdb=" O LEU X 338 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N SER X 340 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU X 77 " --> pdb=" O SER X 340 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 344 through 346 Processing sheet with id=AD1, first strand: chain 'Y' and resid 40 through 41 removed outlier: 3.840A pdb=" N SER Y 41 " --> pdb=" O MET Y 44 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET Y 44 " --> pdb=" O SER Y 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'Y' and resid 98 through 102 removed outlier: 6.396A pdb=" N THR Y 99 " --> pdb=" O PHE Y 294 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASP Y 296 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE Y 101 " --> pdb=" O ASP Y 296 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA Y 70 " --> pdb=" O ILE Y 352 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Y' and resid 126 through 147 removed outlier: 6.908A pdb=" N THR Y 159 " --> pdb=" O VAL Y 141 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE Y 143 " --> pdb=" O LYS Y 157 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS Y 157 " --> pdb=" O ILE Y 143 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE Y 145 " --> pdb=" O GLN Y 155 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLN Y 155 " --> pdb=" O ILE Y 145 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY Y 156 " --> pdb=" O LEU Y 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 166 through 171 current: chain 'Y' and resid 199 through 205 removed outlier: 5.449A pdb=" N VAL Y 222 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG Y 204 " --> pdb=" O VAL Y 222 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Y' and resid 329 through 331 1074 hydrogen bonds defined for protein. 3132 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: 11.17 Time building geometry restraints manager: 7.98 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: 9550 1.34 - 1.46: 5814 1.46 - 1.58: 13554 1.58 - 1.71: 18 1.71 - 1.83: 166 Bond restraints: 29102 Sorted by residual: bond pdb=" N TYR X 229 " pdb=" CA TYR X 229 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 6.11e+00 bond pdb=" N PHE X 222 " pdb=" CA PHE X 222 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.31e-02 5.83e+03 5.67e+00 bond pdb=" N LEU X 224 " pdb=" CA LEU X 224 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.56e+00 bond pdb=" N GLU X 227 " pdb=" CA GLU X 227 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.26e-02 6.30e+03 5.47e+00 bond pdb=" N GLU X 225 " pdb=" CA GLU X 225 " ideal model delta sigma weight residual 1.461 1.489 -0.028 1.20e-02 6.94e+03 5.30e+00 ... (remaining 29097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.71: 39083 3.71 - 7.42: 248 7.42 - 11.14: 33 11.14 - 14.85: 5 14.85 - 18.56: 4 Bond angle restraints: 39373 Sorted by residual: angle pdb=" CB MET W 175 " pdb=" CG MET W 175 " pdb=" SD MET W 175 " ideal model delta sigma weight residual 112.70 130.82 -18.12 3.00e+00 1.11e-01 3.65e+01 angle pdb=" CB MET Q1291 " pdb=" CG MET Q1291 " pdb=" SD MET Q1291 " ideal model delta sigma weight residual 112.70 130.16 -17.46 3.00e+00 1.11e-01 3.39e+01 angle pdb=" CB MET Q1405 " pdb=" CG MET Q1405 " pdb=" SD MET Q1405 " ideal model delta sigma weight residual 112.70 129.37 -16.67 3.00e+00 1.11e-01 3.09e+01 angle pdb=" CA LEU Q 963 " pdb=" CB LEU Q 963 " pdb=" CG LEU Q 963 " ideal model delta sigma weight residual 116.30 134.86 -18.56 3.50e+00 8.16e-02 2.81e+01 angle pdb=" CA MET Q1405 " pdb=" CB MET Q1405 " pdb=" CG MET Q1405 " ideal model delta sigma weight residual 114.10 124.26 -10.16 2.00e+00 2.50e-01 2.58e+01 ... (remaining 39368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.74: 17104 33.74 - 67.49: 721 67.49 - 101.23: 48 101.23 - 134.98: 5 134.98 - 168.72: 2 Dihedral angle restraints: 17880 sinusoidal: 7318 harmonic: 10562 Sorted by residual: dihedral pdb=" C5' ADP U 501 " pdb=" O5' ADP U 501 " pdb=" PA ADP U 501 " pdb=" O2A ADP U 501 " ideal model delta sinusoidal sigma weight residual 300.00 131.28 168.72 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O1B ADP U 501 " pdb=" O3A ADP U 501 " pdb=" PB ADP U 501 " pdb=" PA ADP U 501 " ideal model delta sinusoidal sigma weight residual 300.00 162.10 137.90 1 2.00e+01 2.50e-03 4.18e+01 dihedral pdb=" O1B ADP V 501 " pdb=" O3A ADP V 501 " pdb=" PB ADP V 501 " pdb=" PA ADP V 501 " ideal model delta sinusoidal sigma weight residual 300.00 172.69 127.30 1 2.00e+01 2.50e-03 3.85e+01 ... (remaining 17877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4003 0.072 - 0.144: 565 0.144 - 0.216: 48 0.216 - 0.288: 3 0.288 - 0.360: 1 Chirality restraints: 4620 Sorted by residual: chirality pdb=" CB ILE Q 971 " pdb=" CA ILE Q 971 " pdb=" CG1 ILE Q 971 " pdb=" CG2 ILE Q 971 " both_signs ideal model delta sigma weight residual False 2.64 3.00 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CB VAL Q1152 " pdb=" CA VAL Q1152 " pdb=" CG1 VAL Q1152 " pdb=" CG2 VAL Q1152 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ASP X 352 " pdb=" N ASP X 352 " pdb=" C ASP X 352 " pdb=" CB ASP X 352 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 4617 not shown) Planarity restraints: 5040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN Q1397 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO Q1398 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO Q1398 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO Q1398 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP Y 95 " 0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ASP Y 95 " -0.064 2.00e-02 2.50e+03 pdb=" O ASP Y 95 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL Y 96 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU T 119 " -0.015 2.00e-02 2.50e+03 3.11e-02 9.64e+00 pdb=" CD GLU T 119 " 0.054 2.00e-02 2.50e+03 pdb=" OE1 GLU T 119 " -0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU T 119 " -0.018 2.00e-02 2.50e+03 ... (remaining 5037 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 190 2.54 - 3.13: 20153 3.13 - 3.72: 43773 3.72 - 4.31: 59933 4.31 - 4.90: 101432 Nonbonded interactions: 225481 Sorted by model distance: nonbonded pdb=" NE2 HIS U 153 " pdb=" OE1 GLN U 155 " model vdw 1.956 3.120 nonbonded pdb=" OG SER Y 24 " pdb=" OE2 GLU Y 374 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR T 248 " pdb=" OD1 ASP T 251 " model vdw 2.273 3.040 nonbonded pdb=" O PRO Y 76 " pdb=" OG1 THR Y 79 " model vdw 2.282 3.040 nonbonded pdb=" O LEU Y 255 " pdb=" OG1 THR Y 259 " model vdw 2.285 3.040 ... (remaining 225476 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 'T' and (resid 22 through 463 or resid 501)) selection = (chain 'V' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 463 or resid 501)) selection = (chain 'X' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 463 or resid 501)) } ncs_group { reference = (chain 'U' and (resid 18 through 459 or resid 501)) selection = (chain 'W' and (resid 18 through 210 or resid 221 through 459 or resid 501)) selection = (chain 'Y' and (resid 18 through 210 or resid 221 through 459 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.560 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: 0.020 Extract box with map and model: 1.300 Check model and map are aligned: 0.220 Set scattering table: 0.300 Process input model: 65.230 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 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 0.066 29103 Z= 0.195 Angle : 0.828 18.562 39373 Z= 0.429 Chirality : 0.050 0.360 4620 Planarity : 0.005 0.103 5040 Dihedral : 17.559 168.724 11060 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.03 % Allowed : 25.21 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.12), residues: 3618 helix: -1.49 (0.11), residues: 1493 sheet: 0.73 (0.21), residues: 636 loop : -1.45 (0.14), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q1361 HIS 0.023 0.001 HIS Q1342 PHE 0.025 0.001 PHE Z 293 TYR 0.016 0.002 TYR V 462 ARG 0.006 0.001 ARG V 392 Details of bonding type rmsd hydrogen bonds : bond 0.16915 ( 1074) hydrogen bonds : angle 6.58140 ( 3132) covalent geometry : bond 0.00415 (29102) covalent geometry : angle 0.82789 (39373) Misc. bond : bond 0.00214 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1045 time to evaluate : 3.125 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: Q 1012 ASN cc_start: 0.7654 (t0) cc_final: 0.7433 (t0) REVERT: Q 1016 LEU cc_start: 0.7228 (mt) cc_final: 0.6991 (mt) REVERT: Q 1112 LYS cc_start: 0.8375 (mtpp) cc_final: 0.8076 (mtpp) REVERT: Q 1150 LYS cc_start: 0.7561 (tppt) cc_final: 0.7331 (mmmm) REVERT: Q 1189 SER cc_start: 0.8108 (t) cc_final: 0.7438 (p) REVERT: Q 1228 HIS cc_start: 0.7337 (t-90) cc_final: 0.6766 (t70) REVERT: Q 1244 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7794 (mm-40) REVERT: Q 1255 TYR cc_start: 0.7779 (t80) cc_final: 0.6837 (t80) REVERT: Q 1270 LYS cc_start: 0.7629 (ptmm) cc_final: 0.7222 (ptpp) REVERT: Q 1284 SER cc_start: 0.8021 (p) cc_final: 0.7665 (t) REVERT: Q 1287 SER cc_start: 0.7866 (m) cc_final: 0.7396 (t) REVERT: Q 1300 LYS cc_start: 0.8337 (mttt) cc_final: 0.8135 (mttt) REVERT: Q 1316 HIS cc_start: 0.7760 (m-70) cc_final: 0.7385 (m-70) REVERT: Q 1327 MET cc_start: 0.6067 (mmm) cc_final: 0.5701 (mmm) REVERT: Q 1432 MET cc_start: 0.4327 (tpp) cc_final: 0.4075 (tpp) REVERT: R 19 PRO cc_start: 0.8045 (Cg_exo) cc_final: 0.7660 (Cg_endo) REVERT: R 62 ILE cc_start: 0.7619 (mt) cc_final: 0.7397 (mm) REVERT: R 63 PHE cc_start: 0.7586 (p90) cc_final: 0.7326 (p90) REVERT: R 82 VAL cc_start: 0.7716 (t) cc_final: 0.7370 (t) REVERT: R 85 ASP cc_start: 0.8787 (m-30) cc_final: 0.8555 (m-30) REVERT: R 93 ARG cc_start: 0.8545 (tmm-80) cc_final: 0.8080 (ttp-170) REVERT: R 95 GLN cc_start: 0.8923 (mt0) cc_final: 0.8604 (mt0) REVERT: R 97 ARG cc_start: 0.7842 (ttp-110) cc_final: 0.7540 (ttp-110) REVERT: R 113 GLU cc_start: 0.7666 (tt0) cc_final: 0.7339 (tt0) REVERT: R 145 SER cc_start: 0.6876 (p) cc_final: 0.6543 (t) REVERT: R 146 GLN cc_start: 0.7515 (tt0) cc_final: 0.7218 (tt0) REVERT: R 147 ARG cc_start: 0.7904 (ptp90) cc_final: 0.7595 (ptm160) REVERT: R 164 THR cc_start: 0.6558 (p) cc_final: 0.5465 (m) REVERT: R 182 LYS cc_start: 0.7697 (mmtp) cc_final: 0.7490 (mmmm) REVERT: R 193 ASP cc_start: 0.7438 (p0) cc_final: 0.7205 (p0) REVERT: R 201 ASP cc_start: 0.7728 (m-30) cc_final: 0.7486 (m-30) REVERT: R 240 TYR cc_start: 0.7827 (t80) cc_final: 0.7321 (t80) REVERT: R 242 GLN cc_start: 0.7917 (mt0) cc_final: 0.7503 (mt0) REVERT: R 244 GLU cc_start: 0.7631 (tt0) cc_final: 0.7140 (tt0) REVERT: R 249 ASP cc_start: 0.8010 (m-30) cc_final: 0.7684 (m-30) REVERT: R 256 ASN cc_start: 0.7195 (t0) cc_final: 0.6982 (t0) REVERT: R 258 ASP cc_start: 0.7999 (m-30) cc_final: 0.7780 (m-30) REVERT: R 260 ASP cc_start: 0.7566 (m-30) cc_final: 0.7165 (m-30) REVERT: R 262 GLU cc_start: 0.7775 (mp0) cc_final: 0.7009 (mp0) REVERT: R 264 ILE cc_start: 0.8279 (tt) cc_final: 0.7904 (tp) REVERT: R 269 ASN cc_start: 0.7069 (t0) cc_final: 0.6425 (t0) REVERT: R 273 ASN cc_start: 0.8064 (m110) cc_final: 0.7081 (t0) REVERT: R 277 VAL cc_start: 0.7734 (m) cc_final: 0.7349 (p) REVERT: R 596 ARG cc_start: 0.8151 (mpt180) cc_final: 0.7838 (mmt-90) REVERT: R 616 VAL cc_start: 0.8073 (t) cc_final: 0.7849 (p) REVERT: R 653 GLN cc_start: 0.6791 (tp40) cc_final: 0.6572 (tm-30) REVERT: R 656 LYS cc_start: 0.7130 (tttt) cc_final: 0.6908 (tttt) REVERT: R 677 VAL cc_start: 0.8632 (t) cc_final: 0.8344 (m) REVERT: R 709 ASP cc_start: 0.7179 (m-30) cc_final: 0.6926 (m-30) REVERT: R 724 TYR cc_start: 0.7841 (t80) cc_final: 0.7562 (t80) REVERT: R 726 LYS cc_start: 0.8202 (mptt) cc_final: 0.8000 (mtmm) REVERT: R 729 ILE cc_start: 0.6827 (mm) cc_final: 0.6419 (tp) REVERT: R 735 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7948 (mp0) REVERT: R 736 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7180 (tm-30) REVERT: R 746 LYS cc_start: 0.8768 (mttt) cc_final: 0.8564 (mtpp) REVERT: S 114 LYS cc_start: 0.7893 (mttp) cc_final: 0.7638 (mttp) REVERT: S 121 LEU cc_start: 0.7288 (mt) cc_final: 0.6892 (mt) REVERT: S 157 LYS cc_start: 0.7884 (ttmm) cc_final: 0.7671 (ttmm) REVERT: T 23 ARG cc_start: 0.7650 (mmm160) cc_final: 0.7202 (mtp180) REVERT: T 31 LYS cc_start: 0.8194 (mmtp) cc_final: 0.7978 (mmtm) REVERT: T 99 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7941 (ttpp) REVERT: T 122 MET cc_start: 0.7446 (tpt) cc_final: 0.7149 (mmm) REVERT: T 134 LYS cc_start: 0.8336 (mtpp) cc_final: 0.8101 (mtmm) REVERT: T 180 ARG cc_start: 0.8283 (mtp-110) cc_final: 0.8076 (mtp85) REVERT: T 195 SER cc_start: 0.8064 (m) cc_final: 0.7772 (t) REVERT: T 232 LEU cc_start: 0.8389 (mt) cc_final: 0.8178 (mt) REVERT: T 276 LYS cc_start: 0.7938 (pttt) cc_final: 0.7730 (pttt) REVERT: T 295 TYR cc_start: 0.7769 (m-80) cc_final: 0.7521 (m-80) REVERT: T 302 GLU cc_start: 0.7789 (tt0) cc_final: 0.7506 (tt0) REVERT: T 312 GLU cc_start: 0.7580 (mp0) cc_final: 0.6747 (mp0) REVERT: T 317 ASP cc_start: 0.7727 (t0) cc_final: 0.7141 (t0) REVERT: T 345 THR cc_start: 0.8061 (m) cc_final: 0.7564 (p) REVERT: T 347 VAL cc_start: 0.7954 (t) cc_final: 0.7628 (p) REVERT: T 385 GLU cc_start: 0.7621 (tt0) cc_final: 0.7241 (tm-30) REVERT: T 389 THR cc_start: 0.7040 (m) cc_final: 0.6475 (m) REVERT: T 441 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7274 (tp30) REVERT: U 32 ASP cc_start: 0.7503 (m-30) cc_final: 0.7154 (m-30) REVERT: U 65 THR cc_start: 0.7312 (p) cc_final: 0.7097 (t) REVERT: U 105 GLU cc_start: 0.7971 (tt0) cc_final: 0.7620 (tt0) REVERT: U 107 PHE cc_start: 0.8469 (m-80) cc_final: 0.7887 (m-80) REVERT: U 115 GLU cc_start: 0.7474 (tp30) cc_final: 0.7268 (tp30) REVERT: U 139 GLU cc_start: 0.8079 (tt0) cc_final: 0.7808 (tt0) REVERT: U 142 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6481 (tm-30) REVERT: U 157 LYS cc_start: 0.7655 (mttt) cc_final: 0.7136 (mttm) REVERT: U 176 ILE cc_start: 0.7747 (mt) cc_final: 0.7368 (tt) REVERT: U 193 ASP cc_start: 0.7370 (t0) cc_final: 0.6749 (t0) REVERT: U 198 LYS cc_start: 0.7966 (ttpt) cc_final: 0.7748 (tttm) REVERT: U 199 ILE cc_start: 0.7038 (mt) cc_final: 0.6535 (tt) REVERT: U 228 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6682 (mm-30) REVERT: U 233 LYS cc_start: 0.7343 (mmmt) cc_final: 0.6851 (mmmt) REVERT: U 264 GLU cc_start: 0.7984 (mt-10) cc_final: 0.6836 (mt-10) REVERT: U 282 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7063 (mt-10) REVERT: U 283 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6661 (mt-10) REVERT: U 311 ARG cc_start: 0.7852 (mmt180) cc_final: 0.7648 (mmt180) REVERT: U 322 MET cc_start: 0.7473 (mtt) cc_final: 0.7245 (mtp) REVERT: U 339 SER cc_start: 0.8293 (m) cc_final: 0.8075 (t) REVERT: U 359 TYR cc_start: 0.8176 (m-80) cc_final: 0.7907 (m-80) REVERT: U 374 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7436 (mm-30) REVERT: U 376 GLU cc_start: 0.7376 (pm20) cc_final: 0.7156 (pm20) REVERT: U 379 LEU cc_start: 0.8373 (mt) cc_final: 0.8142 (mt) REVERT: U 385 ASP cc_start: 0.7577 (m-30) cc_final: 0.7374 (m-30) REVERT: U 413 ARG cc_start: 0.7521 (mtm110) cc_final: 0.7229 (ptm-80) REVERT: U 422 ASP cc_start: 0.7995 (m-30) cc_final: 0.7741 (m-30) REVERT: U 432 ASP cc_start: 0.7934 (p0) cc_final: 0.7705 (p0) REVERT: U 438 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7360 (tppt) REVERT: U 439 TYR cc_start: 0.7210 (m-80) cc_final: 0.6812 (m-10) REVERT: U 451 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7149 (mp10) REVERT: V 36 ASP cc_start: 0.6983 (m-30) cc_final: 0.6523 (m-30) REVERT: V 40 VAL cc_start: 0.7212 (t) cc_final: 0.6492 (t) REVERT: V 42 LYS cc_start: 0.7262 (mtmm) cc_final: 0.6429 (tttt) REVERT: V 63 ASP cc_start: 0.7841 (t0) cc_final: 0.7634 (t0) REVERT: V 69 LYS cc_start: 0.7821 (mttm) cc_final: 0.7323 (mtmm) REVERT: V 99 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7619 (mtpt) REVERT: V 177 LYS cc_start: 0.8073 (ttmt) cc_final: 0.7619 (ttpp) REVERT: V 178 THR cc_start: 0.8234 (m) cc_final: 0.7912 (p) REVERT: V 187 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6733 (mm-30) REVERT: V 193 LYS cc_start: 0.7548 (mtpt) cc_final: 0.7295 (mtpt) REVERT: V 203 GLU cc_start: 0.7895 (pt0) cc_final: 0.7463 (mt-10) REVERT: V 214 ARG cc_start: 0.7236 (mmt180) cc_final: 0.6656 (mmm-85) REVERT: V 227 GLU cc_start: 0.7452 (tt0) cc_final: 0.7219 (mm-30) REVERT: V 264 ASP cc_start: 0.6536 (p0) cc_final: 0.6318 (p0) REVERT: V 287 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7538 (mm-30) REVERT: V 294 LYS cc_start: 0.7535 (tppt) cc_final: 0.7330 (tppt) REVERT: V 297 ASP cc_start: 0.7783 (t0) cc_final: 0.7414 (t0) REVERT: V 302 GLU cc_start: 0.7472 (pt0) cc_final: 0.7164 (pt0) REVERT: V 315 MET cc_start: 0.7927 (mmp) cc_final: 0.7726 (mmm) REVERT: V 326 LYS cc_start: 0.7632 (tmmt) cc_final: 0.7166 (tppt) REVERT: V 355 SER cc_start: 0.8631 (m) cc_final: 0.7931 (p) REVERT: V 385 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7126 (mm-30) REVERT: V 392 ARG cc_start: 0.8109 (mtt-85) cc_final: 0.7694 (mtt-85) REVERT: W 38 ARG cc_start: 0.7958 (mtm-85) cc_final: 0.7575 (mtt90) REVERT: W 58 LEU cc_start: 0.7254 (tp) cc_final: 0.7022 (tt) REVERT: W 134 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6641 (mm-30) REVERT: W 142 GLU cc_start: 0.8227 (tt0) cc_final: 0.8022 (tt0) REVERT: W 146 ASP cc_start: 0.8422 (m-30) cc_final: 0.7744 (m-30) REVERT: W 154 LYS cc_start: 0.8277 (mtpp) cc_final: 0.8049 (mtmt) REVERT: W 160 ILE cc_start: 0.8255 (tt) cc_final: 0.7807 (tp) REVERT: W 181 LYS cc_start: 0.8011 (ttpp) cc_final: 0.7727 (ttpp) REVERT: W 189 VAL cc_start: 0.7456 (t) cc_final: 0.7163 (m) REVERT: W 266 ARG cc_start: 0.7151 (mtm-85) cc_final: 0.6615 (mtm-85) REVERT: W 285 LYS cc_start: 0.8112 (ttmm) cc_final: 0.7905 (ttmm) REVERT: W 297 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7560 (mm-30) REVERT: W 302 ASP cc_start: 0.7247 (t0) cc_final: 0.6573 (t0) REVERT: W 304 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6775 (mp0) REVERT: W 311 ARG cc_start: 0.7626 (mmt180) cc_final: 0.7373 (mmp-170) REVERT: W 322 MET cc_start: 0.8074 (ttm) cc_final: 0.7811 (ttm) REVERT: W 330 SER cc_start: 0.8148 (p) cc_final: 0.7906 (p) REVERT: W 333 ARG cc_start: 0.8066 (mtm180) cc_final: 0.7787 (mtm180) REVERT: W 338 LYS cc_start: 0.8271 (mtpt) cc_final: 0.7921 (mtmt) REVERT: W 357 LYS cc_start: 0.7779 (pptt) cc_final: 0.7278 (pptt) REVERT: W 374 GLU cc_start: 0.7371 (tp30) cc_final: 0.7074 (tp30) REVERT: W 376 GLU cc_start: 0.7244 (mp0) cc_final: 0.6909 (mp0) REVERT: W 378 GLU cc_start: 0.7708 (mp0) cc_final: 0.7006 (tm-30) REVERT: W 381 SER cc_start: 0.7618 (m) cc_final: 0.7195 (p) REVERT: W 385 ASP cc_start: 0.7869 (m-30) cc_final: 0.7592 (m-30) REVERT: W 388 THR cc_start: 0.8309 (m) cc_final: 0.8011 (p) REVERT: W 393 GLU cc_start: 0.7857 (tt0) cc_final: 0.7359 (mt-10) REVERT: W 413 ARG cc_start: 0.7702 (mtp180) cc_final: 0.7368 (mtm180) REVERT: W 442 GLU cc_start: 0.6917 (pt0) cc_final: 0.6643 (pp20) REVERT: W 443 ASN cc_start: 0.6549 (m110) cc_final: 0.5663 (m110) REVERT: W 449 ASP cc_start: 0.7343 (t70) cc_final: 0.6915 (t70) REVERT: W 451 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7575 (mm110) REVERT: X 100 VAL cc_start: 0.8098 (t) cc_final: 0.7843 (m) REVERT: X 114 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7566 (mt-10) REVERT: X 141 GLU cc_start: 0.7448 (pm20) cc_final: 0.7035 (pm20) REVERT: X 144 VAL cc_start: 0.8475 (t) cc_final: 0.8144 (p) REVERT: X 172 SER cc_start: 0.8030 (m) cc_final: 0.7743 (t) REVERT: X 177 LYS cc_start: 0.8017 (ttmt) cc_final: 0.7748 (ttmm) REVERT: X 178 THR cc_start: 0.8006 (p) cc_final: 0.7439 (t) REVERT: X 179 LEU cc_start: 0.7742 (mt) cc_final: 0.7449 (mp) REVERT: X 182 ASP cc_start: 0.7659 (t70) cc_final: 0.7459 (m-30) REVERT: X 187 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7484 (mm-30) REVERT: X 196 ILE cc_start: 0.7796 (mt) cc_final: 0.7435 (mm) REVERT: X 198 ASP cc_start: 0.7344 (m-30) cc_final: 0.6698 (m-30) REVERT: X 210 LYS cc_start: 0.7070 (ptmt) cc_final: 0.6831 (ptmt) REVERT: X 221 GLU cc_start: 0.7479 (tp30) cc_final: 0.7096 (tp30) REVERT: X 226 THR cc_start: 0.7280 (OUTLIER) cc_final: 0.7017 (p) REVERT: X 239 LYS cc_start: 0.7904 (pttt) cc_final: 0.7613 (pttm) REVERT: X 240 LYS cc_start: 0.8217 (mtmt) cc_final: 0.8007 (mtmt) REVERT: X 251 ASP cc_start: 0.6906 (m-30) cc_final: 0.6637 (m-30) REVERT: X 282 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6486 (tm-30) REVERT: X 295 TYR cc_start: 0.7781 (m-80) cc_final: 0.7186 (m-80) REVERT: X 315 MET cc_start: 0.7468 (mmp) cc_final: 0.7177 (mmm) REVERT: X 325 ASN cc_start: 0.8304 (m-40) cc_final: 0.7895 (m-40) REVERT: X 341 ASN cc_start: 0.8452 (p0) cc_final: 0.8231 (p0) REVERT: X 345 THR cc_start: 0.8084 (p) cc_final: 0.7754 (p) REVERT: X 348 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7083 (mtm180) REVERT: X 409 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7481 (tm-30) REVERT: X 432 LYS cc_start: 0.8138 (mmmt) cc_final: 0.7624 (mmmm) REVERT: X 434 ILE cc_start: 0.7443 (mt) cc_final: 0.7159 (tt) REVERT: X 438 ASP cc_start: 0.7825 (m-30) cc_final: 0.7570 (m-30) REVERT: Y 34 ASN cc_start: 0.7774 (t0) cc_final: 0.7491 (t0) REVERT: Y 59 LYS cc_start: 0.7871 (ttmm) cc_final: 0.7654 (mmmt) REVERT: Y 107 PHE cc_start: 0.8191 (m-80) cc_final: 0.7826 (m-80) REVERT: Y 115 GLU cc_start: 0.6890 (tm-30) cc_final: 0.6186 (tm-30) REVERT: Y 144 GLN cc_start: 0.6659 (tt0) cc_final: 0.6250 (tt0) REVERT: Y 188 ASP cc_start: 0.7996 (t0) cc_final: 0.7775 (m-30) REVERT: Y 206 PHE cc_start: 0.7800 (m-80) cc_final: 0.7558 (m-80) REVERT: Y 210 ARG cc_start: 0.8060 (mmm160) cc_final: 0.7444 (mmm160) REVERT: Y 264 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7648 (mt-10) REVERT: Y 281 LYS cc_start: 0.7322 (tttm) cc_final: 0.7053 (ttpp) REVERT: Y 316 GLU cc_start: 0.7274 (mt-10) cc_final: 0.7004 (mt-10) REVERT: Y 317 PHE cc_start: 0.8504 (m-80) cc_final: 0.8120 (m-80) REVERT: Y 322 MET cc_start: 0.8264 (mtp) cc_final: 0.8047 (mtm) REVERT: Y 349 ASP cc_start: 0.7848 (t0) cc_final: 0.7630 (t70) REVERT: Y 357 LYS cc_start: 0.7746 (mttm) cc_final: 0.7394 (mmtp) REVERT: Y 361 GLU cc_start: 0.7293 (tt0) cc_final: 0.7057 (tp30) REVERT: Y 373 GLN cc_start: 0.7773 (tt0) cc_final: 0.7572 (tt0) REVERT: Y 374 GLU cc_start: 0.7229 (tt0) cc_final: 0.6486 (tt0) REVERT: Y 378 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6721 (mm-30) REVERT: Y 392 VAL cc_start: 0.7837 (t) cc_final: 0.7433 (p) REVERT: Y 401 ASN cc_start: 0.7937 (m-40) cc_final: 0.7736 (m-40) REVERT: Y 443 ASN cc_start: 0.7712 (m110) cc_final: 0.7359 (m110) REVERT: Y 444 GLU cc_start: 0.7923 (tt0) cc_final: 0.7325 (tp30) REVERT: Y 453 ASN cc_start: 0.8233 (m110) cc_final: 0.7809 (m-40) REVERT: Z 307 ARG cc_start: 0.8097 (ttm-80) cc_final: 0.7861 (tpp80) REVERT: Z 311 ARG cc_start: 0.7966 (ttm110) cc_final: 0.7510 (mtp85) REVERT: Z 312 TYR cc_start: 0.8017 (m-80) cc_final: 0.7740 (m-80) outliers start: 1 outliers final: 0 residues processed: 1045 average time/residue: 0.4599 time to fit residues: 719.2510 Evaluate side-chains 905 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 904 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 226 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 0.0060 chunk 273 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 184 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 210 optimal weight: 0.8980 chunk 327 optimal weight: 2.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1213 ASN Q1342 HIS R 121 HIS R 132 ASN R 175 ASN ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 ASN T 29 HIS T 190 GLN U 274 ASN V 154 ASN V 325 ASN V 417 GLN W 144 GLN W 155 GLN X 271 GLN X 331 ASN Y 25 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.123812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.102669 restraints weight = 46131.061| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.30 r_work: 0.3215 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29103 Z= 0.149 Angle : 0.584 9.369 39373 Z= 0.292 Chirality : 0.044 0.194 4620 Planarity : 0.004 0.065 5040 Dihedral : 7.065 143.867 4005 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.66 % Allowed : 22.97 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.13), residues: 3618 helix: 0.08 (0.13), residues: 1500 sheet: 0.75 (0.20), residues: 656 loop : -1.14 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q1361 HIS 0.010 0.001 HIS Q1342 PHE 0.025 0.001 PHE R 691 TYR 0.020 0.001 TYR R 231 ARG 0.008 0.000 ARG X 132 Details of bonding type rmsd hydrogen bonds : bond 0.04540 ( 1074) hydrogen bonds : angle 4.37377 ( 3132) covalent geometry : bond 0.00343 (29102) covalent geometry : angle 0.58366 (39373) Misc. bond : bond 0.00225 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 932 time to evaluate : 3.538 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: Q 1007 PHE cc_start: 0.7911 (m-80) cc_final: 0.7697 (m-80) REVERT: Q 1112 LYS cc_start: 0.8754 (mtpp) cc_final: 0.8523 (mtpp) REVERT: Q 1146 THR cc_start: 0.8290 (p) cc_final: 0.6837 (m) REVERT: Q 1150 LYS cc_start: 0.8659 (tppt) cc_final: 0.8387 (mmmm) REVERT: Q 1189 SER cc_start: 0.8724 (t) cc_final: 0.8273 (p) REVERT: Q 1195 LYS cc_start: 0.8023 (pptt) cc_final: 0.7701 (pptt) REVERT: Q 1208 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7986 (ptm160) REVERT: Q 1255 TYR cc_start: 0.8687 (t80) cc_final: 0.8211 (t80) REVERT: Q 1284 SER cc_start: 0.8746 (p) cc_final: 0.8492 (t) REVERT: Q 1287 SER cc_start: 0.8695 (m) cc_final: 0.8353 (t) REVERT: Q 1327 MET cc_start: 0.5633 (mmm) cc_final: 0.5127 (mmm) REVERT: Q 1328 MET cc_start: 0.7248 (tpt) cc_final: 0.6954 (tpt) REVERT: R 19 PRO cc_start: 0.8610 (Cg_exo) cc_final: 0.8183 (Cg_endo) REVERT: R 79 PHE cc_start: 0.8211 (m-10) cc_final: 0.7987 (m-80) REVERT: R 93 ARG cc_start: 0.8583 (tmm-80) cc_final: 0.8224 (ttp-170) REVERT: R 100 PHE cc_start: 0.8594 (m-80) cc_final: 0.8335 (m-80) REVERT: R 111 THR cc_start: 0.7386 (p) cc_final: 0.5988 (m) REVERT: R 116 ASP cc_start: 0.7947 (m-30) cc_final: 0.7712 (m-30) REVERT: R 145 SER cc_start: 0.7879 (p) cc_final: 0.7668 (t) REVERT: R 242 GLN cc_start: 0.8453 (mt0) cc_final: 0.8019 (mt0) REVERT: R 244 GLU cc_start: 0.8024 (tt0) cc_final: 0.7706 (tt0) REVERT: R 260 ASP cc_start: 0.8330 (m-30) cc_final: 0.8060 (m-30) REVERT: R 262 GLU cc_start: 0.8011 (mp0) cc_final: 0.7451 (mp0) REVERT: R 264 ILE cc_start: 0.8845 (tt) cc_final: 0.8625 (tp) REVERT: R 269 ASN cc_start: 0.7640 (t0) cc_final: 0.7167 (t0) REVERT: R 677 VAL cc_start: 0.8888 (t) cc_final: 0.8628 (m) REVERT: R 729 ILE cc_start: 0.7516 (mm) cc_final: 0.7019 (mp) REVERT: R 736 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7450 (tm-30) REVERT: T 105 LEU cc_start: 0.8694 (tp) cc_final: 0.8444 (tp) REVERT: T 119 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7711 (tm-30) REVERT: T 122 MET cc_start: 0.8733 (tpt) cc_final: 0.8481 (mmm) REVERT: T 123 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8088 (mt-10) REVERT: T 195 SER cc_start: 0.8694 (m) cc_final: 0.8464 (t) REVERT: T 317 ASP cc_start: 0.7889 (t0) cc_final: 0.7644 (t0) REVERT: T 365 ASP cc_start: 0.7909 (m-30) cc_final: 0.7515 (m-30) REVERT: U 107 PHE cc_start: 0.8810 (m-80) cc_final: 0.8605 (m-80) REVERT: U 115 GLU cc_start: 0.8477 (tp30) cc_final: 0.8176 (tp30) REVERT: U 142 GLU cc_start: 0.7453 (tm-30) cc_final: 0.6818 (tm-30) REVERT: U 144 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6339 (mp10) REVERT: U 157 LYS cc_start: 0.8426 (mttt) cc_final: 0.8002 (mttm) REVERT: U 228 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7524 (mm-30) REVERT: U 233 LYS cc_start: 0.7765 (mmmt) cc_final: 0.7507 (mmmt) REVERT: U 264 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7280 (mt-10) REVERT: U 281 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8506 (tttp) REVERT: U 438 LYS cc_start: 0.8312 (ttpp) cc_final: 0.7856 (tppt) REVERT: V 36 ASP cc_start: 0.7582 (m-30) cc_final: 0.7116 (m-30) REVERT: V 40 VAL cc_start: 0.8430 (t) cc_final: 0.7681 (t) REVERT: V 42 LYS cc_start: 0.7842 (mtmm) cc_final: 0.7307 (tttt) REVERT: V 69 LYS cc_start: 0.8477 (mttm) cc_final: 0.8232 (mtmm) REVERT: V 99 LYS cc_start: 0.8558 (mtpt) cc_final: 0.8277 (mtpt) REVERT: V 178 THR cc_start: 0.8833 (m) cc_final: 0.8560 (p) REVERT: V 180 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8389 (ttp80) REVERT: V 181 LEU cc_start: 0.8568 (mp) cc_final: 0.8365 (mt) REVERT: V 187 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6965 (mm-30) REVERT: V 242 GLU cc_start: 0.8254 (mp0) cc_final: 0.7873 (mp0) REVERT: V 294 LYS cc_start: 0.8741 (tppt) cc_final: 0.8520 (tppt) REVERT: V 297 ASP cc_start: 0.8355 (t0) cc_final: 0.8010 (t0) REVERT: V 336 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8716 (t) REVERT: V 355 SER cc_start: 0.8444 (m) cc_final: 0.8215 (t) REVERT: V 365 ASP cc_start: 0.7961 (m-30) cc_final: 0.7731 (t0) REVERT: V 392 ARG cc_start: 0.8671 (mtt-85) cc_final: 0.8358 (mtt-85) REVERT: V 454 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8510 (ttmm) REVERT: W 38 ARG cc_start: 0.8836 (mtm-85) cc_final: 0.8575 (mtt90) REVERT: W 167 THR cc_start: 0.8807 (p) cc_final: 0.8583 (t) REVERT: W 266 ARG cc_start: 0.7405 (mtm-85) cc_final: 0.7141 (mtm-85) REVERT: W 285 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8533 (ttmm) REVERT: W 302 ASP cc_start: 0.7396 (t0) cc_final: 0.7143 (t0) REVERT: W 357 LYS cc_start: 0.8126 (pptt) cc_final: 0.7827 (pptt) REVERT: W 359 TYR cc_start: 0.8871 (m-80) cc_final: 0.8594 (m-80) REVERT: W 385 ASP cc_start: 0.8018 (m-30) cc_final: 0.7650 (m-30) REVERT: W 388 THR cc_start: 0.8450 (m) cc_final: 0.8148 (p) REVERT: W 413 ARG cc_start: 0.8449 (mtp180) cc_final: 0.8164 (mtm180) REVERT: W 443 ASN cc_start: 0.7763 (m110) cc_final: 0.7513 (m-40) REVERT: W 449 ASP cc_start: 0.8035 (t70) cc_final: 0.7780 (t70) REVERT: X 77 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7436 (pt) REVERT: X 113 VAL cc_start: 0.9091 (m) cc_final: 0.8886 (t) REVERT: X 122 MET cc_start: 0.8878 (tpp) cc_final: 0.8610 (tpt) REVERT: X 134 LYS cc_start: 0.8339 (ptpt) cc_final: 0.8137 (ptpp) REVERT: X 187 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7737 (mm-30) REVERT: X 189 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8328 (mt) REVERT: X 192 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7623 (mt-10) REVERT: X 210 LYS cc_start: 0.7760 (ptmt) cc_final: 0.7462 (ptmt) REVERT: X 211 ARG cc_start: 0.8234 (mtp-110) cc_final: 0.7630 (mtp180) REVERT: X 226 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8110 (p) REVERT: X 228 GLU cc_start: 0.7626 (pt0) cc_final: 0.7248 (pt0) REVERT: X 251 ASP cc_start: 0.7902 (m-30) cc_final: 0.7701 (m-30) REVERT: X 282 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7168 (tp30) REVERT: X 290 LYS cc_start: 0.8216 (ttmm) cc_final: 0.7994 (mtmt) REVERT: X 295 TYR cc_start: 0.8862 (m-80) cc_final: 0.8274 (m-80) REVERT: X 392 ARG cc_start: 0.8230 (mtm110) cc_final: 0.7955 (mtm180) REVERT: X 428 THR cc_start: 0.8590 (t) cc_final: 0.8387 (t) REVERT: Y 59 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8569 (mmtm) REVERT: Y 107 PHE cc_start: 0.8785 (m-80) cc_final: 0.8438 (m-80) REVERT: Y 115 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7325 (tm-30) REVERT: Y 210 ARG cc_start: 0.8052 (mmm160) cc_final: 0.7571 (mmm160) REVERT: Y 264 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7776 (mt-10) REVERT: Y 283 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7623 (mt-10) REVERT: Y 359 TYR cc_start: 0.8561 (m-80) cc_final: 0.8319 (m-80) REVERT: Y 415 ASN cc_start: 0.8137 (t0) cc_final: 0.7491 (t0) REVERT: Y 443 ASN cc_start: 0.8591 (m110) cc_final: 0.8375 (m110) REVERT: Y 444 GLU cc_start: 0.8466 (tt0) cc_final: 0.8258 (tp30) REVERT: Y 449 ASP cc_start: 0.8087 (t70) cc_final: 0.7883 (m-30) REVERT: Y 453 ASN cc_start: 0.8837 (m110) cc_final: 0.8622 (m-40) outliers start: 84 outliers final: 41 residues processed: 969 average time/residue: 0.5229 time to fit residues: 772.0150 Evaluate side-chains 937 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 889 time to evaluate : 4.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1001 ILE Chi-restraints excluded: chain Q residue 1168 LYS Chi-restraints excluded: chain Q residue 1222 GLU Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 263 LYS Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 617 GLU Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 438 ASP Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 350 THR Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 368 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 189 ILE Chi-restraints excluded: chain X residue 226 THR Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 391 GLU Chi-restraints excluded: chain X residue 435 VAL Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 59 LYS Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 458 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 49 optimal weight: 0.9980 chunk 330 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 348 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 199 optimal weight: 0.5980 chunk 272 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS R 144 GLN R 146 GLN R 653 GLN R 749 ASN ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 256 ASN T 331 ASN ** V 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 417 GLN V 427 GLN X 154 ASN X 331 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.121830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.100775 restraints weight = 46037.558| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.30 r_work: 0.3182 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 29103 Z= 0.195 Angle : 0.602 9.003 39373 Z= 0.301 Chirality : 0.045 0.175 4620 Planarity : 0.004 0.052 5040 Dihedral : 7.079 137.154 4005 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.70 % Allowed : 22.68 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3618 helix: 0.54 (0.13), residues: 1507 sheet: 0.72 (0.20), residues: 660 loop : -1.08 (0.15), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q1361 HIS 0.013 0.001 HIS R 121 PHE 0.023 0.002 PHE R 70 TYR 0.019 0.002 TYR Q1198 ARG 0.011 0.001 ARG V 371 Details of bonding type rmsd hydrogen bonds : bond 0.04654 ( 1074) hydrogen bonds : angle 4.21080 ( 3132) covalent geometry : bond 0.00457 (29102) covalent geometry : angle 0.60188 (39373) Misc. bond : bond 0.00531 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 913 time to evaluate : 3.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1007 PHE cc_start: 0.7877 (m-80) cc_final: 0.7633 (m-80) REVERT: Q 1112 LYS cc_start: 0.8729 (mtpp) cc_final: 0.8529 (mtpp) REVERT: Q 1146 THR cc_start: 0.8405 (p) cc_final: 0.7219 (m) REVERT: Q 1165 LEU cc_start: 0.8213 (mm) cc_final: 0.7881 (mt) REVERT: Q 1189 SER cc_start: 0.8670 (t) cc_final: 0.8401 (p) REVERT: Q 1195 LYS cc_start: 0.8023 (pptt) cc_final: 0.7682 (pptt) REVERT: Q 1208 ARG cc_start: 0.8272 (ttm170) cc_final: 0.7978 (ptm160) REVERT: Q 1255 TYR cc_start: 0.8681 (t80) cc_final: 0.8280 (t80) REVERT: Q 1287 SER cc_start: 0.8754 (m) cc_final: 0.8483 (t) REVERT: Q 1327 MET cc_start: 0.5396 (mmm) cc_final: 0.4697 (mmm) REVERT: Q 1328 MET cc_start: 0.7235 (tpt) cc_final: 0.6944 (tpt) REVERT: Q 1331 MET cc_start: 0.8399 (tpp) cc_final: 0.7487 (mpp) REVERT: R 19 PRO cc_start: 0.8592 (Cg_exo) cc_final: 0.8096 (Cg_endo) REVERT: R 93 ARG cc_start: 0.8608 (tmm-80) cc_final: 0.8286 (ttp-170) REVERT: R 242 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7952 (mt0) REVERT: R 260 ASP cc_start: 0.8391 (m-30) cc_final: 0.8047 (m-30) REVERT: R 262 GLU cc_start: 0.7984 (mp0) cc_final: 0.7475 (mp0) REVERT: R 269 ASN cc_start: 0.7701 (t0) cc_final: 0.7229 (t0) REVERT: R 677 VAL cc_start: 0.8908 (t) cc_final: 0.8665 (m) REVERT: R 712 LYS cc_start: 0.7961 (mtpp) cc_final: 0.7729 (mtpp) REVERT: R 723 GLN cc_start: 0.7557 (mp10) cc_final: 0.7316 (mp10) REVERT: R 724 TYR cc_start: 0.8105 (t80) cc_final: 0.7783 (t80) REVERT: R 729 ILE cc_start: 0.7541 (mm) cc_final: 0.7021 (mp) REVERT: R 736 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7440 (tm-30) REVERT: T 105 LEU cc_start: 0.8679 (tp) cc_final: 0.8477 (tp) REVERT: T 119 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7641 (tm-30) REVERT: T 122 MET cc_start: 0.8706 (tpt) cc_final: 0.8468 (mmm) REVERT: T 123 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8097 (mt-10) REVERT: T 365 ASP cc_start: 0.7979 (m-30) cc_final: 0.7606 (m-30) REVERT: U 115 GLU cc_start: 0.8472 (tp30) cc_final: 0.8163 (tp30) REVERT: U 142 GLU cc_start: 0.7448 (tm-30) cc_final: 0.6961 (tm-30) REVERT: U 144 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.6621 (mp10) REVERT: U 157 LYS cc_start: 0.8497 (mttt) cc_final: 0.8110 (mttm) REVERT: U 176 ILE cc_start: 0.8780 (mt) cc_final: 0.8527 (tt) REVERT: U 193 ASP cc_start: 0.8149 (t0) cc_final: 0.7874 (t0) REVERT: U 228 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7575 (mm-30) REVERT: U 233 LYS cc_start: 0.7790 (mmmt) cc_final: 0.7567 (mmmt) REVERT: U 264 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7412 (mm-30) REVERT: U 279 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8203 (pt0) REVERT: U 281 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8587 (tttp) REVERT: U 282 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7639 (mt-10) REVERT: U 283 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7667 (mt-10) REVERT: U 314 GLU cc_start: 0.8497 (mp0) cc_final: 0.8295 (mp0) REVERT: U 374 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7827 (mm-30) REVERT: U 438 LYS cc_start: 0.8355 (ttpp) cc_final: 0.8136 (tppt) REVERT: U 439 TYR cc_start: 0.7867 (m-80) cc_final: 0.7373 (m-80) REVERT: V 36 ASP cc_start: 0.7561 (m-30) cc_final: 0.7130 (m-30) REVERT: V 40 VAL cc_start: 0.8505 (t) cc_final: 0.7810 (t) REVERT: V 42 LYS cc_start: 0.7984 (mtmm) cc_final: 0.7415 (tttt) REVERT: V 69 LYS cc_start: 0.8590 (mttm) cc_final: 0.8311 (mtmm) REVERT: V 99 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8359 (mtpt) REVERT: V 135 GLU cc_start: 0.7412 (tt0) cc_final: 0.7192 (tt0) REVERT: V 178 THR cc_start: 0.8795 (m) cc_final: 0.8554 (p) REVERT: V 181 LEU cc_start: 0.8640 (mp) cc_final: 0.8416 (mt) REVERT: V 264 ASP cc_start: 0.7819 (p0) cc_final: 0.7600 (p0) REVERT: V 294 LYS cc_start: 0.8735 (tppt) cc_final: 0.8511 (tppt) REVERT: V 297 ASP cc_start: 0.8377 (t0) cc_final: 0.8020 (t0) REVERT: V 336 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8702 (t) REVERT: V 355 SER cc_start: 0.8464 (m) cc_final: 0.8227 (t) REVERT: V 454 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8504 (ttmm) REVERT: W 38 ARG cc_start: 0.8814 (mtm-85) cc_final: 0.8437 (mtt90) REVERT: W 167 THR cc_start: 0.8819 (p) cc_final: 0.8593 (t) REVERT: W 266 ARG cc_start: 0.7420 (mtm-85) cc_final: 0.7202 (mtm-85) REVERT: W 374 GLU cc_start: 0.8105 (tp30) cc_final: 0.7866 (tp30) REVERT: W 378 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7505 (tm-30) REVERT: W 388 THR cc_start: 0.8540 (m) cc_final: 0.8286 (p) REVERT: W 413 ARG cc_start: 0.8486 (mtp180) cc_final: 0.8176 (mtm-85) REVERT: W 443 ASN cc_start: 0.7884 (m110) cc_final: 0.7635 (m-40) REVERT: W 449 ASP cc_start: 0.8054 (t70) cc_final: 0.7840 (t70) REVERT: X 77 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7683 (pp) REVERT: X 122 MET cc_start: 0.8868 (tpp) cc_final: 0.8661 (tpt) REVERT: X 171 LYS cc_start: 0.8570 (tttt) cc_final: 0.8279 (ttpt) REVERT: X 187 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7763 (mm-30) REVERT: X 190 GLN cc_start: 0.8685 (mt0) cc_final: 0.8482 (mt0) REVERT: X 192 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7653 (mt-10) REVERT: X 210 LYS cc_start: 0.7993 (ptmt) cc_final: 0.7607 (ptmt) REVERT: X 211 ARG cc_start: 0.8296 (mtp-110) cc_final: 0.7710 (mtp180) REVERT: X 226 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8012 (p) REVERT: X 240 LYS cc_start: 0.8407 (mtmt) cc_final: 0.8196 (mtmm) REVERT: X 276 LYS cc_start: 0.8006 (tmtt) cc_final: 0.7642 (tmtt) REVERT: X 282 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7505 (tp30) REVERT: X 290 LYS cc_start: 0.8284 (ttmm) cc_final: 0.8043 (mtmt) REVERT: X 295 TYR cc_start: 0.8999 (m-80) cc_final: 0.8767 (m-80) REVERT: X 428 THR cc_start: 0.8654 (t) cc_final: 0.8450 (t) REVERT: X 432 LYS cc_start: 0.8425 (mmmm) cc_final: 0.8096 (mmmm) REVERT: Y 59 LYS cc_start: 0.8818 (ttmm) cc_final: 0.8574 (tptp) REVERT: Y 115 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7268 (tm-30) REVERT: Y 210 ARG cc_start: 0.8103 (mmm160) cc_final: 0.7694 (mmm160) REVERT: Y 283 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7668 (mt-10) REVERT: Y 415 ASN cc_start: 0.8182 (t0) cc_final: 0.7507 (t0) REVERT: Y 443 ASN cc_start: 0.8615 (m110) cc_final: 0.8388 (m110) REVERT: Y 444 GLU cc_start: 0.8449 (tt0) cc_final: 0.8248 (tp30) REVERT: Y 449 ASP cc_start: 0.8107 (t70) cc_final: 0.7886 (m-30) REVERT: Y 458 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.8039 (pt) REVERT: Z 311 ARG cc_start: 0.8629 (mtp85) cc_final: 0.8283 (mtp85) outliers start: 117 outliers final: 69 residues processed: 971 average time/residue: 0.4542 time to fit residues: 666.4231 Evaluate side-chains 970 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 893 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1001 ILE Chi-restraints excluded: chain Q residue 1168 LYS Chi-restraints excluded: chain Q residue 1242 ILE Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 263 LYS Chi-restraints excluded: chain R residue 595 LEU Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 617 GLU Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 241 LYS Chi-restraints excluded: chain T residue 314 ASN Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain T residue 433 GLU Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 235 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 296 ASP Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 274 LYS Chi-restraints excluded: chain V residue 317 ASP Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 350 THR Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 368 LEU Chi-restraints excluded: chain W residue 402 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 226 THR Chi-restraints excluded: chain X residue 264 ASP Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 389 THR Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 357 LYS Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 458 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 327 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 177 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 231 optimal weight: 0.7980 chunk 274 optimal weight: 1.9990 chunk 332 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 312 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1316 HIS R 107 ASN R 121 HIS R 144 GLN R 146 GLN R 659 GLN S 65 GLN T 331 ASN U 230 GLN U 272 GLN V 325 ASN V 394 GLN ** W 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 154 ASN X 331 ASN Y 62 GLN Y 453 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.122076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.100967 restraints weight = 46165.108| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.30 r_work: 0.3188 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29103 Z= 0.157 Angle : 0.585 8.217 39373 Z= 0.289 Chirality : 0.044 0.235 4620 Planarity : 0.004 0.059 5040 Dihedral : 6.920 131.326 4005 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.89 % Allowed : 23.13 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3618 helix: 0.79 (0.14), residues: 1509 sheet: 0.68 (0.20), residues: 668 loop : -1.05 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP Q1361 HIS 0.012 0.001 HIS V 165 PHE 0.022 0.001 PHE R 691 TYR 0.019 0.002 TYR R 34 ARG 0.012 0.000 ARG V 180 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 1074) hydrogen bonds : angle 4.10641 ( 3132) covalent geometry : bond 0.00367 (29102) covalent geometry : angle 0.58488 (39373) Misc. bond : bond 0.00857 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 919 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1007 PHE cc_start: 0.7875 (m-80) cc_final: 0.7632 (m-80) REVERT: Q 1189 SER cc_start: 0.8615 (t) cc_final: 0.8326 (p) REVERT: Q 1195 LYS cc_start: 0.8007 (pptt) cc_final: 0.7655 (pptt) REVERT: Q 1208 ARG cc_start: 0.8296 (ttm170) cc_final: 0.7940 (ptm160) REVERT: Q 1255 TYR cc_start: 0.8693 (t80) cc_final: 0.8389 (t80) REVERT: Q 1287 SER cc_start: 0.8772 (m) cc_final: 0.8496 (t) REVERT: Q 1327 MET cc_start: 0.5504 (mmm) cc_final: 0.4998 (mmm) REVERT: Q 1328 MET cc_start: 0.7225 (tpt) cc_final: 0.6936 (tpt) REVERT: Q 1331 MET cc_start: 0.8409 (tpp) cc_final: 0.7721 (mpp) REVERT: Q 1432 MET cc_start: 0.5583 (tpp) cc_final: 0.5011 (tpp) REVERT: R 93 ARG cc_start: 0.8622 (tmm-80) cc_final: 0.8354 (ttp-170) REVERT: R 144 GLN cc_start: 0.7418 (pt0) cc_final: 0.7188 (pt0) REVERT: R 242 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7935 (mt0) REVERT: R 260 ASP cc_start: 0.8351 (m-30) cc_final: 0.8030 (m-30) REVERT: R 262 GLU cc_start: 0.7983 (mp0) cc_final: 0.7473 (mp0) REVERT: R 269 ASN cc_start: 0.7718 (t0) cc_final: 0.7240 (t0) REVERT: R 677 VAL cc_start: 0.8870 (t) cc_final: 0.8633 (m) REVERT: R 712 LYS cc_start: 0.7921 (mtpp) cc_final: 0.7703 (mtpp) REVERT: R 723 GLN cc_start: 0.7266 (mp10) cc_final: 0.6773 (mp10) REVERT: R 724 TYR cc_start: 0.7979 (t80) cc_final: 0.7507 (t80) REVERT: R 729 ILE cc_start: 0.7540 (mm) cc_final: 0.7060 (mp) REVERT: R 736 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7448 (tm-30) REVERT: S 77 LEU cc_start: 0.8483 (mm) cc_final: 0.8247 (mp) REVERT: T 105 LEU cc_start: 0.8663 (tp) cc_final: 0.8450 (tp) REVERT: T 122 MET cc_start: 0.8724 (tpt) cc_final: 0.8469 (mmm) REVERT: T 317 ASP cc_start: 0.7915 (t0) cc_final: 0.7677 (t0) REVERT: T 362 ASP cc_start: 0.8089 (t0) cc_final: 0.7884 (m-30) REVERT: T 365 ASP cc_start: 0.7970 (m-30) cc_final: 0.7684 (m-30) REVERT: U 115 GLU cc_start: 0.8449 (tp30) cc_final: 0.8151 (tp30) REVERT: U 142 GLU cc_start: 0.7393 (tm-30) cc_final: 0.6915 (tm-30) REVERT: U 144 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.6628 (mp10) REVERT: U 157 LYS cc_start: 0.8486 (mttt) cc_final: 0.8112 (mttm) REVERT: U 176 ILE cc_start: 0.8742 (mt) cc_final: 0.8506 (tt) REVERT: U 193 ASP cc_start: 0.8177 (t0) cc_final: 0.7890 (t0) REVERT: U 233 LYS cc_start: 0.7815 (mmmt) cc_final: 0.7611 (mmmt) REVERT: U 264 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7390 (tt0) REVERT: U 279 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8205 (pt0) REVERT: U 281 LYS cc_start: 0.8960 (ttmm) cc_final: 0.8620 (tttp) REVERT: U 282 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7642 (mt-10) REVERT: U 283 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7667 (mt-10) REVERT: U 316 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: U 374 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7979 (mm-30) REVERT: U 437 VAL cc_start: 0.8931 (m) cc_final: 0.8667 (p) REVERT: U 439 TYR cc_start: 0.7666 (m-80) cc_final: 0.7428 (m-80) REVERT: V 36 ASP cc_start: 0.7585 (m-30) cc_final: 0.7149 (m-30) REVERT: V 40 VAL cc_start: 0.8562 (t) cc_final: 0.7948 (t) REVERT: V 42 LYS cc_start: 0.8024 (mtmm) cc_final: 0.7496 (tttt) REVERT: V 69 LYS cc_start: 0.8590 (mttm) cc_final: 0.8271 (mtmm) REVERT: V 99 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8369 (mtpt) REVERT: V 178 THR cc_start: 0.8775 (m) cc_final: 0.8553 (p) REVERT: V 181 LEU cc_start: 0.8625 (mp) cc_final: 0.8394 (mt) REVERT: V 264 ASP cc_start: 0.7776 (p0) cc_final: 0.7529 (p0) REVERT: V 294 LYS cc_start: 0.8729 (tppt) cc_final: 0.8518 (tppt) REVERT: V 297 ASP cc_start: 0.8416 (t0) cc_final: 0.8058 (t0) REVERT: V 336 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8687 (t) REVERT: V 355 SER cc_start: 0.8422 (m) cc_final: 0.8192 (t) REVERT: V 454 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8518 (ttmm) REVERT: W 38 ARG cc_start: 0.8797 (mtm-85) cc_final: 0.8468 (mtt90) REVERT: W 167 THR cc_start: 0.8809 (p) cc_final: 0.8589 (t) REVERT: W 266 ARG cc_start: 0.7408 (mtm-85) cc_final: 0.7174 (mtm-85) REVERT: W 378 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7479 (tm-30) REVERT: W 388 THR cc_start: 0.8571 (m) cc_final: 0.8298 (p) REVERT: W 413 ARG cc_start: 0.8478 (mtp180) cc_final: 0.8173 (mtm-85) REVERT: W 443 ASN cc_start: 0.7836 (m110) cc_final: 0.7587 (m-40) REVERT: X 75 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8202 (pt) REVERT: X 77 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7649 (pp) REVERT: X 122 MET cc_start: 0.8857 (tpp) cc_final: 0.8655 (tpt) REVERT: X 192 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7665 (mt-10) REVERT: X 210 LYS cc_start: 0.8061 (ptmt) cc_final: 0.7659 (ptmt) REVERT: X 211 ARG cc_start: 0.8272 (mtp-110) cc_final: 0.7675 (mtp180) REVERT: X 228 GLU cc_start: 0.7820 (pt0) cc_final: 0.7494 (pt0) REVERT: X 268 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7929 (mtm) REVERT: X 276 LYS cc_start: 0.7903 (tmtt) cc_final: 0.7570 (tmtt) REVERT: X 282 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7512 (tp30) REVERT: X 290 LYS cc_start: 0.8248 (ttmm) cc_final: 0.8009 (mtmt) REVERT: X 440 ASN cc_start: 0.7943 (m110) cc_final: 0.7566 (m110) REVERT: Y 59 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8553 (tptp) REVERT: Y 115 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7270 (tm-30) REVERT: Y 210 ARG cc_start: 0.8151 (mmm160) cc_final: 0.7784 (mmm160) REVERT: Y 302 ASP cc_start: 0.7704 (m-30) cc_final: 0.7300 (m-30) REVERT: Y 415 ASN cc_start: 0.8209 (t0) cc_final: 0.7534 (t0) REVERT: Y 444 GLU cc_start: 0.8455 (tt0) cc_final: 0.8253 (tp30) REVERT: Y 449 ASP cc_start: 0.8076 (t70) cc_final: 0.7870 (m-30) REVERT: Y 458 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.8012 (pt) outliers start: 123 outliers final: 78 residues processed: 974 average time/residue: 0.4954 time to fit residues: 733.7135 Evaluate side-chains 979 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 890 time to evaluate : 3.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1001 ILE Chi-restraints excluded: chain Q residue 1150 LYS Chi-restraints excluded: chain Q residue 1168 LYS Chi-restraints excluded: chain Q residue 1175 LEU Chi-restraints excluded: chain Q residue 1242 ILE Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain Q residue 1361 TRP Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 146 GLN Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 263 LYS Chi-restraints excluded: chain R residue 595 LEU Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 617 GLU Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 145 LYS Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain T residue 241 LYS Chi-restraints excluded: chain T residue 314 ASN Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain T residue 433 GLU Chi-restraints excluded: chain T residue 448 ASP Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 86 MET Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 222 VAL Chi-restraints excluded: chain U residue 235 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 316 GLU Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 225 GLU Chi-restraints excluded: chain V residue 243 ILE Chi-restraints excluded: chain V residue 274 LYS Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 317 ASP Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 350 THR Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 315 ASP Chi-restraints excluded: chain W residue 346 ASP Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 368 LEU Chi-restraints excluded: chain W residue 402 LEU Chi-restraints excluded: chain W residue 429 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 226 THR Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain Y residue 59 LYS Chi-restraints excluded: chain Y residue 94 LYS Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 357 LYS Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 458 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 167 optimal weight: 0.9980 chunk 187 optimal weight: 0.0470 chunk 289 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 267 optimal weight: 1.9990 chunk 190 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 317 optimal weight: 0.0060 chunk 40 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 chunk 126 optimal weight: 0.5980 overall best weight: 0.4294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1316 HIS R 121 HIS R 613 HIS R 666 ASN T 256 ASN T 331 ASN T 437 ASN U 272 GLN V 165 HIS V 325 ASN W 173 ASN X 331 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.122943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.101892 restraints weight = 46206.427| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.30 r_work: 0.3202 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29103 Z= 0.117 Angle : 0.560 9.251 39373 Z= 0.275 Chirality : 0.043 0.215 4620 Planarity : 0.004 0.046 5040 Dihedral : 6.693 128.031 4005 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.70 % Allowed : 23.51 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3618 helix: 0.98 (0.14), residues: 1500 sheet: 0.71 (0.20), residues: 660 loop : -0.95 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP Q1361 HIS 0.014 0.001 HIS R 121 PHE 0.022 0.001 PHE R 691 TYR 0.017 0.001 TYR U 427 ARG 0.011 0.000 ARG R 97 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 1074) hydrogen bonds : angle 3.99717 ( 3132) covalent geometry : bond 0.00270 (29102) covalent geometry : angle 0.55969 (39373) Misc. bond : bond 0.00619 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 899 time to evaluate : 3.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1007 PHE cc_start: 0.7863 (m-80) cc_final: 0.7614 (m-80) REVERT: Q 1189 SER cc_start: 0.8592 (t) cc_final: 0.8303 (p) REVERT: Q 1195 LYS cc_start: 0.7982 (pptt) cc_final: 0.7617 (pptt) REVERT: Q 1208 ARG cc_start: 0.8286 (ttm170) cc_final: 0.7903 (ptm160) REVERT: Q 1255 TYR cc_start: 0.8658 (t80) cc_final: 0.8359 (t80) REVERT: Q 1287 SER cc_start: 0.8755 (m) cc_final: 0.8473 (t) REVERT: Q 1327 MET cc_start: 0.5573 (mmm) cc_final: 0.5034 (mmm) REVERT: Q 1328 MET cc_start: 0.7226 (tpt) cc_final: 0.6890 (tpt) REVERT: Q 1331 MET cc_start: 0.8398 (tpp) cc_final: 0.7670 (mpp) REVERT: Q 1432 MET cc_start: 0.5517 (tpp) cc_final: 0.4955 (tpp) REVERT: R 34 TYR cc_start: 0.8078 (t80) cc_final: 0.7627 (t80) REVERT: R 93 ARG cc_start: 0.8603 (tmm-80) cc_final: 0.8319 (ttp-170) REVERT: R 116 ASP cc_start: 0.7846 (m-30) cc_final: 0.7646 (m-30) REVERT: R 242 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7914 (mt0) REVERT: R 260 ASP cc_start: 0.8311 (m-30) cc_final: 0.8011 (m-30) REVERT: R 262 GLU cc_start: 0.8019 (mp0) cc_final: 0.7477 (mp0) REVERT: R 269 ASN cc_start: 0.7615 (t0) cc_final: 0.7123 (t0) REVERT: R 677 VAL cc_start: 0.8849 (t) cc_final: 0.8627 (m) REVERT: R 712 LYS cc_start: 0.7867 (mtpp) cc_final: 0.7615 (mtpp) REVERT: R 723 GLN cc_start: 0.7245 (mp10) cc_final: 0.6750 (mp10) REVERT: R 724 TYR cc_start: 0.7903 (t80) cc_final: 0.7308 (t80) REVERT: R 729 ILE cc_start: 0.7502 (mm) cc_final: 0.7071 (mp) REVERT: R 736 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7416 (tm-30) REVERT: T 105 LEU cc_start: 0.8665 (tp) cc_final: 0.8464 (tp) REVERT: T 122 MET cc_start: 0.8715 (tpt) cc_final: 0.8449 (mmm) REVERT: T 362 ASP cc_start: 0.8077 (t0) cc_final: 0.7873 (m-30) REVERT: T 365 ASP cc_start: 0.7945 (m-30) cc_final: 0.7610 (m-30) REVERT: U 115 GLU cc_start: 0.8465 (tp30) cc_final: 0.8163 (tp30) REVERT: U 131 GLU cc_start: 0.7481 (pt0) cc_final: 0.7269 (pt0) REVERT: U 142 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6856 (tm-30) REVERT: U 144 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.6581 (mp10) REVERT: U 157 LYS cc_start: 0.8445 (mttt) cc_final: 0.8065 (mttm) REVERT: U 176 ILE cc_start: 0.8731 (mt) cc_final: 0.8511 (tt) REVERT: U 193 ASP cc_start: 0.8146 (t0) cc_final: 0.7823 (t0) REVERT: U 264 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7374 (tt0) REVERT: U 279 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8171 (pt0) REVERT: U 281 LYS cc_start: 0.8934 (ttmm) cc_final: 0.8610 (tttp) REVERT: U 282 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7606 (mt-10) REVERT: U 283 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7626 (mt-10) REVERT: U 374 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7996 (mm-30) REVERT: U 413 ARG cc_start: 0.8255 (mtm110) cc_final: 0.7957 (ptm-80) REVERT: U 437 VAL cc_start: 0.8904 (m) cc_final: 0.8681 (p) REVERT: V 36 ASP cc_start: 0.7581 (m-30) cc_final: 0.7181 (m-30) REVERT: V 40 VAL cc_start: 0.8552 (t) cc_final: 0.7956 (t) REVERT: V 42 LYS cc_start: 0.8056 (mtmm) cc_final: 0.7471 (tttp) REVERT: V 69 LYS cc_start: 0.8560 (mttm) cc_final: 0.8280 (mtmm) REVERT: V 99 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8331 (mtpt) REVERT: V 135 GLU cc_start: 0.7367 (tt0) cc_final: 0.7157 (tt0) REVERT: V 181 LEU cc_start: 0.8652 (mp) cc_final: 0.8427 (mt) REVERT: V 264 ASP cc_start: 0.7779 (p0) cc_final: 0.7553 (p0) REVERT: V 294 LYS cc_start: 0.8723 (tppt) cc_final: 0.8500 (tppt) REVERT: V 297 ASP cc_start: 0.8356 (t0) cc_final: 0.8010 (t0) REVERT: V 355 SER cc_start: 0.8390 (m) cc_final: 0.8176 (t) REVERT: V 454 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8507 (ttmm) REVERT: W 38 ARG cc_start: 0.8794 (mtm-85) cc_final: 0.8570 (mtt90) REVERT: W 167 THR cc_start: 0.8787 (p) cc_final: 0.8565 (t) REVERT: W 266 ARG cc_start: 0.7391 (mtm-85) cc_final: 0.7160 (mtm-85) REVERT: W 378 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7512 (tm-30) REVERT: W 388 THR cc_start: 0.8544 (m) cc_final: 0.8258 (p) REVERT: W 413 ARG cc_start: 0.8451 (mtp180) cc_final: 0.8151 (mtm-85) REVERT: W 443 ASN cc_start: 0.7819 (m110) cc_final: 0.7576 (m-40) REVERT: X 75 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8106 (pt) REVERT: X 77 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7635 (pp) REVERT: X 192 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7734 (mt-10) REVERT: X 210 LYS cc_start: 0.8041 (ptmt) cc_final: 0.7648 (ptmt) REVERT: X 211 ARG cc_start: 0.8276 (mtp-110) cc_final: 0.7623 (mtp180) REVERT: X 226 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8080 (p) REVERT: X 228 GLU cc_start: 0.7866 (pt0) cc_final: 0.7495 (pt0) REVERT: X 276 LYS cc_start: 0.7877 (tmtt) cc_final: 0.7568 (tmtt) REVERT: X 282 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7555 (tp30) REVERT: X 290 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7972 (mtmt) REVERT: X 428 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8468 (t) REVERT: X 440 ASN cc_start: 0.7944 (m110) cc_final: 0.7528 (m110) REVERT: Y 59 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8527 (tptp) REVERT: Y 115 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: Y 210 ARG cc_start: 0.8104 (mmm160) cc_final: 0.7745 (mmm160) REVERT: Y 415 ASN cc_start: 0.8169 (t0) cc_final: 0.7428 (t0) REVERT: Y 444 GLU cc_start: 0.8423 (tt0) cc_final: 0.8213 (tp30) REVERT: Y 449 ASP cc_start: 0.8051 (t70) cc_final: 0.7842 (m-30) REVERT: Y 458 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8050 (pt) outliers start: 117 outliers final: 77 residues processed: 956 average time/residue: 0.4510 time to fit residues: 648.9192 Evaluate side-chains 990 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 902 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1150 LYS Chi-restraints excluded: chain Q residue 1168 LYS Chi-restraints excluded: chain Q residue 1175 LEU Chi-restraints excluded: chain Q residue 1242 ILE Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 263 LYS Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 595 LEU Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 617 GLU Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 145 LYS Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain T residue 433 GLU Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 86 MET Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 222 VAL Chi-restraints excluded: chain U residue 235 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 243 ILE Chi-restraints excluded: chain V residue 274 LYS Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 350 THR Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 338 LYS Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 368 LEU Chi-restraints excluded: chain W residue 402 LEU Chi-restraints excluded: chain W residue 429 LEU Chi-restraints excluded: chain W residue 444 GLU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 226 THR Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 389 THR Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain X residue 434 ILE Chi-restraints excluded: chain X residue 435 VAL Chi-restraints excluded: chain Y residue 59 LYS Chi-restraints excluded: chain Y residue 94 LYS Chi-restraints excluded: chain Y residue 115 GLU Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 357 LYS Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 458 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 165 optimal weight: 0.7980 chunk 300 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 306 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 318 optimal weight: 1.9990 chunk 345 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 GLN R 146 GLN R 666 ASN ** R 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 331 ASN T 437 ASN U 272 GLN ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 455 GLN V 165 HIS V 325 ASN V 417 GLN W 173 ASN X 154 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.121553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.100384 restraints weight = 46339.500| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.33 r_work: 0.3179 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29103 Z= 0.165 Angle : 0.591 9.877 39373 Z= 0.293 Chirality : 0.044 0.192 4620 Planarity : 0.004 0.051 5040 Dihedral : 6.679 127.279 4005 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.64 % Allowed : 24.17 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3618 helix: 0.98 (0.14), residues: 1508 sheet: 0.68 (0.20), residues: 661 loop : -0.95 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q1361 HIS 0.023 0.001 HIS R 121 PHE 0.023 0.001 PHE R 70 TYR 0.019 0.002 TYR Q1198 ARG 0.013 0.000 ARG R 97 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 1074) hydrogen bonds : angle 4.03747 ( 3132) covalent geometry : bond 0.00385 (29102) covalent geometry : angle 0.59113 (39373) Misc. bond : bond 0.00610 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 921 time to evaluate : 3.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1007 PHE cc_start: 0.7814 (m-80) cc_final: 0.7555 (m-80) REVERT: Q 1189 SER cc_start: 0.8588 (t) cc_final: 0.8280 (p) REVERT: Q 1195 LYS cc_start: 0.7959 (pptt) cc_final: 0.7582 (pptt) REVERT: Q 1208 ARG cc_start: 0.8327 (ttm170) cc_final: 0.8059 (tpp80) REVERT: Q 1255 TYR cc_start: 0.8691 (t80) cc_final: 0.8372 (t80) REVERT: Q 1287 SER cc_start: 0.8768 (m) cc_final: 0.8477 (t) REVERT: Q 1327 MET cc_start: 0.5782 (mmm) cc_final: 0.5225 (mmm) REVERT: Q 1328 MET cc_start: 0.7319 (tpt) cc_final: 0.7036 (tpt) REVERT: Q 1331 MET cc_start: 0.8375 (tpp) cc_final: 0.7654 (mpp) REVERT: Q 1432 MET cc_start: 0.5478 (tpp) cc_final: 0.4905 (tpp) REVERT: R 93 ARG cc_start: 0.8685 (tmm-80) cc_final: 0.8358 (ttp-170) REVERT: R 242 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7943 (mt0) REVERT: R 260 ASP cc_start: 0.8315 (m-30) cc_final: 0.7991 (m-30) REVERT: R 262 GLU cc_start: 0.8055 (mp0) cc_final: 0.7473 (mp0) REVERT: R 269 ASN cc_start: 0.7566 (t0) cc_final: 0.7047 (t0) REVERT: R 608 GLU cc_start: 0.8222 (tt0) cc_final: 0.7249 (tt0) REVERT: R 677 VAL cc_start: 0.8867 (t) cc_final: 0.8602 (m) REVERT: R 712 LYS cc_start: 0.7845 (mtpp) cc_final: 0.7597 (mtpp) REVERT: R 723 GLN cc_start: 0.7228 (mp10) cc_final: 0.6661 (mp10) REVERT: R 724 TYR cc_start: 0.7837 (t80) cc_final: 0.7238 (t80) REVERT: R 729 ILE cc_start: 0.7447 (mm) cc_final: 0.7224 (tp) REVERT: R 736 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7450 (tm-30) REVERT: T 105 LEU cc_start: 0.8665 (tp) cc_final: 0.8454 (tp) REVERT: T 122 MET cc_start: 0.8687 (tpt) cc_final: 0.8422 (mmm) REVERT: T 365 ASP cc_start: 0.7976 (m-30) cc_final: 0.7626 (m-30) REVERT: U 115 GLU cc_start: 0.8484 (tp30) cc_final: 0.8171 (tp30) REVERT: U 131 GLU cc_start: 0.7543 (pt0) cc_final: 0.7280 (pt0) REVERT: U 142 GLU cc_start: 0.7419 (tm-30) cc_final: 0.6833 (tm-30) REVERT: U 144 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6529 (mp10) REVERT: U 157 LYS cc_start: 0.8472 (mttt) cc_final: 0.7986 (mttm) REVERT: U 170 GLU cc_start: 0.8053 (tp30) cc_final: 0.7797 (tp30) REVERT: U 176 ILE cc_start: 0.8675 (mt) cc_final: 0.8474 (tt) REVERT: U 193 ASP cc_start: 0.8201 (t0) cc_final: 0.7844 (t0) REVERT: U 264 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7467 (tt0) REVERT: U 279 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8216 (pt0) REVERT: U 281 LYS cc_start: 0.8946 (ttmm) cc_final: 0.8613 (tttp) REVERT: U 282 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7689 (mt-10) REVERT: U 283 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7715 (mt-10) REVERT: U 316 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7489 (mm-30) REVERT: U 374 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7915 (mm-30) REVERT: U 413 ARG cc_start: 0.8305 (mtm110) cc_final: 0.7966 (ptm-80) REVERT: U 437 VAL cc_start: 0.8867 (m) cc_final: 0.8641 (p) REVERT: V 36 ASP cc_start: 0.7607 (m-30) cc_final: 0.7217 (m-30) REVERT: V 40 VAL cc_start: 0.8551 (t) cc_final: 0.7988 (t) REVERT: V 42 LYS cc_start: 0.8064 (mtmm) cc_final: 0.7382 (tttp) REVERT: V 69 LYS cc_start: 0.8572 (mttm) cc_final: 0.8293 (mtpp) REVERT: V 99 LYS cc_start: 0.8637 (mtpt) cc_final: 0.8363 (mtpt) REVERT: V 135 GLU cc_start: 0.7389 (tt0) cc_final: 0.7143 (tt0) REVERT: V 153 GLU cc_start: 0.7907 (pm20) cc_final: 0.7658 (pm20) REVERT: V 242 GLU cc_start: 0.8309 (mp0) cc_final: 0.7718 (mp0) REVERT: V 264 ASP cc_start: 0.7749 (p0) cc_final: 0.7517 (p0) REVERT: V 294 LYS cc_start: 0.8680 (tppt) cc_final: 0.8457 (tppt) REVERT: V 297 ASP cc_start: 0.8370 (t0) cc_final: 0.8024 (t0) REVERT: V 336 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8697 (t) REVERT: V 355 SER cc_start: 0.8378 (m) cc_final: 0.8122 (t) REVERT: V 400 LEU cc_start: 0.8758 (mt) cc_final: 0.8507 (mt) REVERT: V 454 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8486 (ttmm) REVERT: W 38 ARG cc_start: 0.8810 (mtm-85) cc_final: 0.8440 (mtt90) REVERT: W 167 THR cc_start: 0.8804 (p) cc_final: 0.8556 (t) REVERT: W 266 ARG cc_start: 0.7476 (mtm-85) cc_final: 0.7247 (mtm-85) REVERT: W 378 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7492 (tm-30) REVERT: W 388 THR cc_start: 0.8593 (m) cc_final: 0.8294 (p) REVERT: W 395 SER cc_start: 0.8570 (t) cc_final: 0.8299 (m) REVERT: W 413 ARG cc_start: 0.8469 (mtp180) cc_final: 0.8139 (mtm180) REVERT: W 443 ASN cc_start: 0.7860 (m110) cc_final: 0.7609 (m-40) REVERT: X 77 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7209 (pt) REVERT: X 192 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7714 (mt-10) REVERT: X 210 LYS cc_start: 0.8123 (ptmt) cc_final: 0.7769 (ptmt) REVERT: X 211 ARG cc_start: 0.8329 (mtp-110) cc_final: 0.7695 (mtp180) REVERT: X 226 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8025 (p) REVERT: X 228 GLU cc_start: 0.7892 (pt0) cc_final: 0.7480 (pt0) REVERT: X 276 LYS cc_start: 0.7940 (tmtt) cc_final: 0.7599 (tmtt) REVERT: X 290 LYS cc_start: 0.8281 (ttmm) cc_final: 0.8023 (mtmt) REVERT: X 428 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8473 (t) REVERT: X 440 ASN cc_start: 0.7913 (m110) cc_final: 0.7471 (m110) REVERT: Y 115 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: Y 210 ARG cc_start: 0.8184 (mmm160) cc_final: 0.7819 (mmm160) REVERT: Y 235 VAL cc_start: 0.8546 (t) cc_final: 0.8344 (m) REVERT: Y 415 ASN cc_start: 0.8207 (t0) cc_final: 0.7521 (t0) REVERT: Y 417 THR cc_start: 0.8585 (p) cc_final: 0.8195 (t) REVERT: Y 444 GLU cc_start: 0.8450 (tt0) cc_final: 0.8247 (tp30) REVERT: Y 458 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8235 (pt) outliers start: 115 outliers final: 84 residues processed: 975 average time/residue: 0.4644 time to fit residues: 685.9019 Evaluate side-chains 998 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 904 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1168 LYS Chi-restraints excluded: chain Q residue 1242 ILE Chi-restraints excluded: chain Q residue 1267 ASP Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain Q residue 1301 LEU Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 146 GLN Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 595 LEU Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 617 GLU Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain R residue 750 THR Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain S residue 145 LYS Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain T residue 314 ASN Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 86 MET Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 222 VAL Chi-restraints excluded: chain U residue 235 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 302 ASP Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 225 GLU Chi-restraints excluded: chain V residue 243 ILE Chi-restraints excluded: chain V residue 274 LYS Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 350 THR Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 315 ASP Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 368 LEU Chi-restraints excluded: chain W residue 402 LEU Chi-restraints excluded: chain W residue 429 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 226 THR Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 389 THR Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain X residue 434 ILE Chi-restraints excluded: chain Y residue 94 LYS Chi-restraints excluded: chain Y residue 115 GLU Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 357 LYS Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 458 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 187 optimal weight: 0.9990 chunk 300 optimal weight: 1.9990 chunk 18 optimal weight: 0.0870 chunk 307 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 332 optimal weight: 0.0770 chunk 269 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 306 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1316 HIS R 121 HIS R 146 GLN R 666 ASN ** R 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 256 ASN T 437 ASN U 272 GLN ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 325 ASN V 417 GLN W 173 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.121313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.100428 restraints weight = 46189.694| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.28 r_work: 0.3175 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29103 Z= 0.167 Angle : 0.596 9.830 39373 Z= 0.295 Chirality : 0.044 0.166 4620 Planarity : 0.004 0.078 5040 Dihedral : 6.676 125.806 4005 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.76 % Allowed : 24.07 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.14), residues: 3618 helix: 0.98 (0.14), residues: 1509 sheet: 0.69 (0.20), residues: 655 loop : -0.91 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q1361 HIS 0.011 0.001 HIS V 165 PHE 0.022 0.001 PHE R 691 TYR 0.020 0.002 TYR Q1198 ARG 0.015 0.000 ARG R 97 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 1074) hydrogen bonds : angle 4.01179 ( 3132) covalent geometry : bond 0.00393 (29102) covalent geometry : angle 0.59605 (39373) Misc. bond : bond 0.00609 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 906 time to evaluate : 3.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1007 PHE cc_start: 0.7837 (m-80) cc_final: 0.7585 (m-80) REVERT: Q 1189 SER cc_start: 0.8579 (t) cc_final: 0.8311 (p) REVERT: Q 1195 LYS cc_start: 0.7925 (pptt) cc_final: 0.7577 (pptt) REVERT: Q 1208 ARG cc_start: 0.8329 (ttm170) cc_final: 0.8091 (tpp80) REVERT: Q 1239 ASP cc_start: 0.7889 (t0) cc_final: 0.7688 (t0) REVERT: Q 1255 TYR cc_start: 0.8691 (t80) cc_final: 0.8431 (t80) REVERT: Q 1287 SER cc_start: 0.8784 (m) cc_final: 0.8430 (t) REVERT: Q 1327 MET cc_start: 0.5827 (mmm) cc_final: 0.5307 (mmm) REVERT: Q 1328 MET cc_start: 0.7291 (tpt) cc_final: 0.7012 (tpt) REVERT: Q 1331 MET cc_start: 0.8360 (tpp) cc_final: 0.7662 (mpp) REVERT: Q 1432 MET cc_start: 0.5448 (tpp) cc_final: 0.5005 (tpp) REVERT: R 93 ARG cc_start: 0.8652 (tmm-80) cc_final: 0.8322 (ttp-170) REVERT: R 260 ASP cc_start: 0.8331 (m-30) cc_final: 0.8037 (m-30) REVERT: R 262 GLU cc_start: 0.8046 (mp0) cc_final: 0.7514 (mp0) REVERT: R 269 ASN cc_start: 0.7546 (t0) cc_final: 0.7091 (t0) REVERT: R 608 GLU cc_start: 0.8180 (tt0) cc_final: 0.7245 (tt0) REVERT: R 612 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7461 (mpp) REVERT: R 677 VAL cc_start: 0.8880 (t) cc_final: 0.8589 (m) REVERT: R 712 LYS cc_start: 0.7891 (mtpp) cc_final: 0.7638 (mtpp) REVERT: R 723 GLN cc_start: 0.7227 (mp10) cc_final: 0.6636 (mp10) REVERT: R 724 TYR cc_start: 0.7873 (t80) cc_final: 0.7344 (t80) REVERT: R 736 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7414 (tm-30) REVERT: S 47 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7042 (ttm110) REVERT: T 122 MET cc_start: 0.8721 (tpt) cc_final: 0.8451 (mmm) REVERT: T 365 ASP cc_start: 0.8001 (m-30) cc_final: 0.7665 (m-30) REVERT: T 430 ASN cc_start: 0.8504 (p0) cc_final: 0.8277 (p0) REVERT: U 115 GLU cc_start: 0.8497 (tp30) cc_final: 0.8192 (tp30) REVERT: U 131 GLU cc_start: 0.7518 (pt0) cc_final: 0.7270 (pt0) REVERT: U 142 GLU cc_start: 0.7424 (tm-30) cc_final: 0.6881 (tm-30) REVERT: U 144 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6597 (mp10) REVERT: U 157 LYS cc_start: 0.8465 (mttt) cc_final: 0.8000 (mtpt) REVERT: U 170 GLU cc_start: 0.8053 (tp30) cc_final: 0.7792 (tp30) REVERT: U 193 ASP cc_start: 0.8183 (t0) cc_final: 0.7847 (t0) REVERT: U 264 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7452 (tt0) REVERT: U 279 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8189 (pt0) REVERT: U 281 LYS cc_start: 0.8984 (ttmm) cc_final: 0.8662 (tttp) REVERT: U 282 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7720 (mt-10) REVERT: U 283 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7689 (mt-10) REVERT: U 316 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7457 (mm-30) REVERT: U 374 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7857 (mm-30) REVERT: U 413 ARG cc_start: 0.8320 (mtm110) cc_final: 0.8019 (ptm-80) REVERT: U 437 VAL cc_start: 0.8907 (m) cc_final: 0.8698 (p) REVERT: V 36 ASP cc_start: 0.7617 (m-30) cc_final: 0.7261 (m-30) REVERT: V 40 VAL cc_start: 0.8621 (t) cc_final: 0.8111 (t) REVERT: V 42 LYS cc_start: 0.8074 (mtmm) cc_final: 0.7486 (tttp) REVERT: V 69 LYS cc_start: 0.8571 (mttm) cc_final: 0.8313 (mtpp) REVERT: V 99 LYS cc_start: 0.8615 (mtpt) cc_final: 0.8360 (mtpt) REVERT: V 135 GLU cc_start: 0.7392 (tt0) cc_final: 0.7133 (tt0) REVERT: V 153 GLU cc_start: 0.7909 (pm20) cc_final: 0.7672 (pm20) REVERT: V 177 LYS cc_start: 0.8926 (ttpp) cc_final: 0.8472 (ttpp) REVERT: V 242 GLU cc_start: 0.8288 (mp0) cc_final: 0.7738 (mp0) REVERT: V 264 ASP cc_start: 0.7774 (p0) cc_final: 0.7538 (p0) REVERT: V 294 LYS cc_start: 0.8743 (tppt) cc_final: 0.8521 (tppt) REVERT: V 297 ASP cc_start: 0.8359 (t0) cc_final: 0.8023 (t0) REVERT: V 355 SER cc_start: 0.8337 (m) cc_final: 0.8126 (t) REVERT: V 454 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8510 (ttmm) REVERT: W 38 ARG cc_start: 0.8805 (mtm-85) cc_final: 0.8449 (mtt90) REVERT: W 167 THR cc_start: 0.8805 (p) cc_final: 0.8547 (t) REVERT: W 378 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7450 (tm-30) REVERT: W 388 THR cc_start: 0.8628 (m) cc_final: 0.8335 (p) REVERT: W 395 SER cc_start: 0.8585 (t) cc_final: 0.8300 (m) REVERT: W 413 ARG cc_start: 0.8478 (mtp180) cc_final: 0.8156 (mtm180) REVERT: W 443 ASN cc_start: 0.7906 (m110) cc_final: 0.7674 (m-40) REVERT: W 449 ASP cc_start: 0.7968 (t70) cc_final: 0.7689 (p0) REVERT: X 192 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7682 (mt-10) REVERT: X 210 LYS cc_start: 0.8161 (ptmt) cc_final: 0.7862 (ptmt) REVERT: X 211 ARG cc_start: 0.8335 (mtp-110) cc_final: 0.7794 (mtp180) REVERT: X 226 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8048 (p) REVERT: X 228 GLU cc_start: 0.7862 (pt0) cc_final: 0.7505 (pt0) REVERT: X 276 LYS cc_start: 0.7981 (tmtt) cc_final: 0.7695 (tmtt) REVERT: X 290 LYS cc_start: 0.8254 (ttmm) cc_final: 0.8012 (mtmt) REVERT: X 428 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8470 (t) REVERT: Y 59 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8554 (tptp) REVERT: Y 115 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: Y 210 ARG cc_start: 0.8213 (mmm160) cc_final: 0.7882 (mmm160) REVERT: Y 415 ASN cc_start: 0.8220 (t0) cc_final: 0.7567 (t0) REVERT: Y 417 THR cc_start: 0.8648 (p) cc_final: 0.8283 (t) REVERT: Y 444 GLU cc_start: 0.8459 (tt0) cc_final: 0.8254 (tp30) REVERT: Y 458 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8256 (pt) outliers start: 119 outliers final: 88 residues processed: 960 average time/residue: 0.4667 time to fit residues: 674.9713 Evaluate side-chains 984 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 886 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1168 LYS Chi-restraints excluded: chain Q residue 1242 ILE Chi-restraints excluded: chain Q residue 1267 ASP Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain Q residue 1301 LEU Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 261 ILE Chi-restraints excluded: chain R residue 595 LEU Chi-restraints excluded: chain R residue 612 MET Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 617 GLU Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain R residue 722 GLU Chi-restraints excluded: chain R residue 750 THR Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain T residue 314 ASN Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 86 MET Chi-restraints excluded: chain U residue 104 SER Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 134 GLU Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 222 VAL Chi-restraints excluded: chain U residue 235 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 225 GLU Chi-restraints excluded: chain V residue 243 ILE Chi-restraints excluded: chain V residue 274 LYS Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 350 THR Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 315 ASP Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 368 LEU Chi-restraints excluded: chain W residue 402 LEU Chi-restraints excluded: chain W residue 429 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 226 THR Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 389 THR Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain X residue 434 ILE Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain Y residue 59 LYS Chi-restraints excluded: chain Y residue 94 LYS Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 115 GLU Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 357 LYS Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 458 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 160 optimal weight: 1.9990 chunk 291 optimal weight: 0.0970 chunk 112 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 254 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 218 optimal weight: 0.9980 chunk 245 optimal weight: 0.0010 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1316 HIS ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS R 146 GLN R 666 ASN ** R 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 417 GLN T 437 ASN U 272 GLN ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 417 GLN W 173 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.121566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.100712 restraints weight = 46229.921| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.27 r_work: 0.3197 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29103 Z= 0.129 Angle : 0.594 9.160 39373 Z= 0.291 Chirality : 0.043 0.175 4620 Planarity : 0.004 0.083 5040 Dihedral : 6.608 122.243 4005 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.39 % Allowed : 24.68 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3618 helix: 1.09 (0.14), residues: 1497 sheet: 0.71 (0.20), residues: 652 loop : -0.84 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q1361 HIS 0.015 0.001 HIS R 121 PHE 0.022 0.001 PHE R 691 TYR 0.021 0.001 TYR Q1337 ARG 0.016 0.000 ARG R 97 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 1074) hydrogen bonds : angle 3.94772 ( 3132) covalent geometry : bond 0.00302 (29102) covalent geometry : angle 0.59373 (39373) Misc. bond : bond 0.01195 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 904 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1007 PHE cc_start: 0.7804 (m-80) cc_final: 0.7550 (m-80) REVERT: Q 1189 SER cc_start: 0.8548 (t) cc_final: 0.8270 (p) REVERT: Q 1195 LYS cc_start: 0.7911 (pptt) cc_final: 0.7555 (pptt) REVERT: Q 1208 ARG cc_start: 0.8298 (ttm170) cc_final: 0.7906 (ptm160) REVERT: Q 1239 ASP cc_start: 0.7884 (t0) cc_final: 0.7679 (t0) REVERT: Q 1255 TYR cc_start: 0.8683 (t80) cc_final: 0.8361 (t80) REVERT: Q 1287 SER cc_start: 0.8787 (m) cc_final: 0.8404 (t) REVERT: Q 1327 MET cc_start: 0.5880 (mmm) cc_final: 0.5337 (mmm) REVERT: Q 1328 MET cc_start: 0.7269 (tpt) cc_final: 0.6997 (tpt) REVERT: Q 1331 MET cc_start: 0.8358 (tpp) cc_final: 0.7689 (mpp) REVERT: Q 1432 MET cc_start: 0.5424 (tpp) cc_final: 0.5011 (tpp) REVERT: R 19 PRO cc_start: 0.8590 (Cg_exo) cc_final: 0.8001 (Cg_endo) REVERT: R 93 ARG cc_start: 0.8612 (tmm-80) cc_final: 0.8190 (ttp-170) REVERT: R 121 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.6984 (t-90) REVERT: R 260 ASP cc_start: 0.8280 (m-30) cc_final: 0.7980 (m-30) REVERT: R 262 GLU cc_start: 0.8017 (mp0) cc_final: 0.7477 (mp0) REVERT: R 269 ASN cc_start: 0.7475 (t0) cc_final: 0.7029 (t0) REVERT: R 608 GLU cc_start: 0.8178 (tt0) cc_final: 0.7274 (tt0) REVERT: R 612 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7433 (mpp) REVERT: R 677 VAL cc_start: 0.8861 (t) cc_final: 0.8557 (m) REVERT: R 712 LYS cc_start: 0.7842 (mtpp) cc_final: 0.7602 (mtpp) REVERT: R 723 GLN cc_start: 0.7170 (mp10) cc_final: 0.6569 (mp10) REVERT: R 724 TYR cc_start: 0.7792 (t80) cc_final: 0.7153 (t80) REVERT: R 736 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7393 (tm-30) REVERT: S 47 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7048 (ttm110) REVERT: T 122 MET cc_start: 0.8686 (tpt) cc_final: 0.8433 (mmm) REVERT: T 365 ASP cc_start: 0.7976 (m-30) cc_final: 0.7626 (m-30) REVERT: T 417 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7767 (mt0) REVERT: U 105 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7779 (mt-10) REVERT: U 115 GLU cc_start: 0.8451 (tp30) cc_final: 0.8149 (tp30) REVERT: U 131 GLU cc_start: 0.7503 (pt0) cc_final: 0.7273 (pt0) REVERT: U 142 GLU cc_start: 0.7419 (tm-30) cc_final: 0.6636 (tm-30) REVERT: U 144 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6117 (mp10) REVERT: U 157 LYS cc_start: 0.8432 (mttt) cc_final: 0.7729 (mtpt) REVERT: U 193 ASP cc_start: 0.8143 (t0) cc_final: 0.7794 (t0) REVERT: U 264 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7459 (tt0) REVERT: U 279 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8180 (pt0) REVERT: U 281 LYS cc_start: 0.8931 (ttmm) cc_final: 0.8601 (tttp) REVERT: U 282 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7687 (mt-10) REVERT: U 283 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7628 (mt-10) REVERT: U 316 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7353 (mm-30) REVERT: U 374 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7782 (mm-30) REVERT: U 376 GLU cc_start: 0.7672 (pm20) cc_final: 0.7112 (pm20) REVERT: U 437 VAL cc_start: 0.8880 (m) cc_final: 0.8666 (p) REVERT: V 36 ASP cc_start: 0.7615 (m-30) cc_final: 0.7262 (m-30) REVERT: V 40 VAL cc_start: 0.8624 (t) cc_final: 0.8127 (t) REVERT: V 42 LYS cc_start: 0.8089 (mtmm) cc_final: 0.7509 (tttp) REVERT: V 69 LYS cc_start: 0.8497 (mttm) cc_final: 0.8276 (mtpp) REVERT: V 99 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8353 (mtpt) REVERT: V 135 GLU cc_start: 0.7363 (tt0) cc_final: 0.7115 (tt0) REVERT: V 144 VAL cc_start: 0.8606 (t) cc_final: 0.8252 (m) REVERT: V 153 GLU cc_start: 0.7902 (pm20) cc_final: 0.7677 (pm20) REVERT: V 177 LYS cc_start: 0.8922 (ttpp) cc_final: 0.8462 (ttpp) REVERT: V 242 GLU cc_start: 0.8295 (mp0) cc_final: 0.7726 (mp0) REVERT: V 264 ASP cc_start: 0.7775 (p0) cc_final: 0.7536 (p0) REVERT: V 294 LYS cc_start: 0.8721 (tppt) cc_final: 0.8497 (tppt) REVERT: V 297 ASP cc_start: 0.8364 (t0) cc_final: 0.8029 (t0) REVERT: V 355 SER cc_start: 0.8322 (m) cc_final: 0.8119 (t) REVERT: V 454 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8500 (ttmm) REVERT: W 38 ARG cc_start: 0.8803 (mtm-85) cc_final: 0.8529 (mtt90) REVERT: W 167 THR cc_start: 0.8804 (p) cc_final: 0.8541 (t) REVERT: W 378 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7487 (tm-30) REVERT: W 388 THR cc_start: 0.8606 (m) cc_final: 0.8309 (p) REVERT: W 395 SER cc_start: 0.8581 (t) cc_final: 0.8296 (m) REVERT: W 413 ARG cc_start: 0.8470 (mtp180) cc_final: 0.8143 (mtm180) REVERT: W 443 ASN cc_start: 0.7870 (m110) cc_final: 0.7636 (m-40) REVERT: W 449 ASP cc_start: 0.7969 (t70) cc_final: 0.7688 (p0) REVERT: X 143 GLU cc_start: 0.8163 (tt0) cc_final: 0.7933 (tt0) REVERT: X 192 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7616 (mt-10) REVERT: X 210 LYS cc_start: 0.8153 (ptmt) cc_final: 0.7826 (ptmt) REVERT: X 211 ARG cc_start: 0.8329 (mtp-110) cc_final: 0.7749 (mtp180) REVERT: X 228 GLU cc_start: 0.7874 (pt0) cc_final: 0.7504 (pt0) REVERT: X 276 LYS cc_start: 0.7965 (tmtt) cc_final: 0.7679 (tmtt) REVERT: X 290 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7990 (mtmt) REVERT: X 385 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8239 (tt0) REVERT: X 428 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8464 (t) REVERT: Y 59 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8543 (tptp) REVERT: Y 115 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: Y 210 ARG cc_start: 0.8205 (mmm160) cc_final: 0.7883 (mmm160) REVERT: Y 248 ASN cc_start: 0.8702 (m-40) cc_final: 0.8421 (m-40) REVERT: Y 415 ASN cc_start: 0.8205 (t0) cc_final: 0.7539 (t0) REVERT: Y 417 THR cc_start: 0.8612 (p) cc_final: 0.8241 (t) REVERT: Y 458 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8256 (pt) outliers start: 107 outliers final: 84 residues processed: 953 average time/residue: 0.4945 time to fit residues: 716.2110 Evaluate side-chains 976 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 881 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1168 LYS Chi-restraints excluded: chain Q residue 1242 ILE Chi-restraints excluded: chain Q residue 1267 ASP Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 146 GLN Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 261 ILE Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 595 LEU Chi-restraints excluded: chain R residue 612 MET Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 617 GLU Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain S residue 47 ARG Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain T residue 314 ASN Chi-restraints excluded: chain T residue 417 GLN Chi-restraints excluded: chain T residue 433 GLU Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 86 MET Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 222 VAL Chi-restraints excluded: chain U residue 235 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain U residue 458 ILE Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 243 ILE Chi-restraints excluded: chain V residue 274 LYS Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 317 ASP Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 350 THR Chi-restraints excluded: chain V residue 373 LEU Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 266 ARG Chi-restraints excluded: chain W residue 338 LYS Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 368 LEU Chi-restraints excluded: chain W residue 402 LEU Chi-restraints excluded: chain W residue 429 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 226 THR Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 389 THR Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain X residue 434 ILE Chi-restraints excluded: chain Y residue 59 LYS Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 115 GLU Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 357 LYS Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 458 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 2.9990 chunk 262 optimal weight: 0.5980 chunk 282 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 245 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 241 optimal weight: 0.7980 chunk 338 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1316 HIS ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS R 146 GLN R 666 ASN ** R 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 ASN T 256 ASN T 437 ASN U 272 GLN ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 325 ASN V 417 GLN W 173 ASN X 331 ASN Y 62 GLN Y 408 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.121169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100294 restraints weight = 45986.395| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.27 r_work: 0.3178 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29103 Z= 0.168 Angle : 0.616 8.938 39373 Z= 0.302 Chirality : 0.045 0.180 4620 Planarity : 0.004 0.074 5040 Dihedral : 6.629 122.976 4005 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.61 % Allowed : 24.74 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3618 helix: 1.04 (0.14), residues: 1501 sheet: 0.65 (0.20), residues: 655 loop : -0.88 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q1361 HIS 0.013 0.001 HIS V 165 PHE 0.022 0.001 PHE R 691 TYR 0.033 0.002 TYR X 323 ARG 0.015 0.000 ARG R 97 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 1074) hydrogen bonds : angle 3.98684 ( 3132) covalent geometry : bond 0.00398 (29102) covalent geometry : angle 0.61583 (39373) Misc. bond : bond 0.01214 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 884 time to evaluate : 3.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1007 PHE cc_start: 0.7833 (m-80) cc_final: 0.7571 (m-80) REVERT: Q 1189 SER cc_start: 0.8577 (t) cc_final: 0.8311 (p) REVERT: Q 1195 LYS cc_start: 0.7909 (pptt) cc_final: 0.7507 (pptt) REVERT: Q 1208 ARG cc_start: 0.8326 (ttm170) cc_final: 0.8086 (tpp80) REVERT: Q 1255 TYR cc_start: 0.8693 (t80) cc_final: 0.8404 (t80) REVERT: Q 1287 SER cc_start: 0.8803 (m) cc_final: 0.8435 (t) REVERT: Q 1327 MET cc_start: 0.5855 (mmm) cc_final: 0.5342 (mmm) REVERT: Q 1328 MET cc_start: 0.7239 (tpt) cc_final: 0.6957 (tpt) REVERT: Q 1331 MET cc_start: 0.8365 (tpp) cc_final: 0.7723 (mpp) REVERT: Q 1432 MET cc_start: 0.5451 (tpp) cc_final: 0.5041 (tpp) REVERT: R 19 PRO cc_start: 0.8594 (Cg_exo) cc_final: 0.8004 (Cg_endo) REVERT: R 93 ARG cc_start: 0.8602 (tmm-80) cc_final: 0.8191 (ttp-170) REVERT: R 121 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.7189 (t-90) REVERT: R 242 GLN cc_start: 0.8204 (mt0) cc_final: 0.7891 (mt0) REVERT: R 260 ASP cc_start: 0.8299 (m-30) cc_final: 0.8000 (m-30) REVERT: R 262 GLU cc_start: 0.8015 (mp0) cc_final: 0.7484 (mp0) REVERT: R 269 ASN cc_start: 0.7476 (t0) cc_final: 0.7053 (t0) REVERT: R 608 GLU cc_start: 0.8172 (tt0) cc_final: 0.7291 (tt0) REVERT: R 612 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7474 (mpp) REVERT: R 677 VAL cc_start: 0.8876 (t) cc_final: 0.8570 (m) REVERT: R 712 LYS cc_start: 0.7874 (mtpp) cc_final: 0.7629 (mtpp) REVERT: R 723 GLN cc_start: 0.7102 (mp10) cc_final: 0.6528 (mp10) REVERT: R 724 TYR cc_start: 0.7798 (t80) cc_final: 0.7270 (t80) REVERT: R 736 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7394 (tm-30) REVERT: T 122 MET cc_start: 0.8708 (tpt) cc_final: 0.8449 (mmm) REVERT: T 365 ASP cc_start: 0.7966 (m-30) cc_final: 0.7600 (m-30) REVERT: T 430 ASN cc_start: 0.8516 (p0) cc_final: 0.8295 (p0) REVERT: U 105 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7782 (mt-10) REVERT: U 115 GLU cc_start: 0.8479 (tp30) cc_final: 0.8176 (tp30) REVERT: U 131 GLU cc_start: 0.7516 (pt0) cc_final: 0.7282 (pt0) REVERT: U 144 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6856 (mt0) REVERT: U 157 LYS cc_start: 0.8449 (mttt) cc_final: 0.8018 (mtpt) REVERT: U 170 GLU cc_start: 0.8057 (tp30) cc_final: 0.7788 (tp30) REVERT: U 193 ASP cc_start: 0.8142 (t0) cc_final: 0.7813 (t0) REVERT: U 264 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7489 (tt0) REVERT: U 279 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8196 (pt0) REVERT: U 281 LYS cc_start: 0.8976 (ttmm) cc_final: 0.8657 (tttp) REVERT: U 282 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7735 (mt-10) REVERT: U 283 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7659 (mt-10) REVERT: U 316 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7355 (mm-30) REVERT: U 374 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7747 (tm-30) REVERT: U 413 ARG cc_start: 0.8268 (mtm110) cc_final: 0.8004 (ptm-80) REVERT: U 437 VAL cc_start: 0.8901 (m) cc_final: 0.8692 (p) REVERT: U 458 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8231 (pt) REVERT: V 42 LYS cc_start: 0.8086 (mtmm) cc_final: 0.7485 (tttt) REVERT: V 69 LYS cc_start: 0.8510 (mttm) cc_final: 0.8278 (mtmm) REVERT: V 99 LYS cc_start: 0.8629 (mtpt) cc_final: 0.8391 (mtpt) REVERT: V 135 GLU cc_start: 0.7360 (tt0) cc_final: 0.7111 (tt0) REVERT: V 144 VAL cc_start: 0.8617 (t) cc_final: 0.8268 (m) REVERT: V 153 GLU cc_start: 0.7899 (pm20) cc_final: 0.7675 (pm20) REVERT: V 177 LYS cc_start: 0.8938 (ttpp) cc_final: 0.8474 (ttpp) REVERT: V 242 GLU cc_start: 0.8273 (mp0) cc_final: 0.7704 (mp0) REVERT: V 264 ASP cc_start: 0.7807 (p0) cc_final: 0.7567 (p0) REVERT: V 294 LYS cc_start: 0.8736 (tppt) cc_final: 0.8523 (tppt) REVERT: V 297 ASP cc_start: 0.8354 (t0) cc_final: 0.8027 (t0) REVERT: V 355 SER cc_start: 0.8345 (m) cc_final: 0.8135 (t) REVERT: V 429 SER cc_start: 0.9068 (m) cc_final: 0.8858 (t) REVERT: V 454 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8547 (ttmm) REVERT: W 38 ARG cc_start: 0.8804 (mtm-85) cc_final: 0.8537 (mtt90) REVERT: W 167 THR cc_start: 0.8828 (p) cc_final: 0.8552 (t) REVERT: W 359 TYR cc_start: 0.8917 (m-80) cc_final: 0.8569 (m-80) REVERT: W 378 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7467 (tm-30) REVERT: W 388 THR cc_start: 0.8641 (m) cc_final: 0.8346 (p) REVERT: W 395 SER cc_start: 0.8597 (t) cc_final: 0.8298 (m) REVERT: W 413 ARG cc_start: 0.8494 (mtp180) cc_final: 0.8169 (mtm180) REVERT: W 443 ASN cc_start: 0.7898 (m110) cc_final: 0.7665 (m-40) REVERT: W 449 ASP cc_start: 0.7983 (t70) cc_final: 0.7710 (p0) REVERT: X 143 GLU cc_start: 0.8202 (tt0) cc_final: 0.7981 (tt0) REVERT: X 192 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7568 (mt-10) REVERT: X 210 LYS cc_start: 0.8197 (ptmt) cc_final: 0.7860 (ptmt) REVERT: X 211 ARG cc_start: 0.8345 (mtp-110) cc_final: 0.7755 (mtp180) REVERT: X 226 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8112 (p) REVERT: X 228 GLU cc_start: 0.7910 (pt0) cc_final: 0.7521 (pt0) REVERT: X 276 LYS cc_start: 0.7990 (tmtt) cc_final: 0.7698 (tmtt) REVERT: X 290 LYS cc_start: 0.8227 (ttmm) cc_final: 0.7986 (mtmt) REVERT: X 367 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8598 (pp) REVERT: X 385 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8272 (tt0) REVERT: X 428 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8479 (t) REVERT: Y 115 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: Y 210 ARG cc_start: 0.8249 (mmm160) cc_final: 0.7933 (mmm160) REVERT: Y 248 ASN cc_start: 0.8732 (m-40) cc_final: 0.8458 (m-40) REVERT: Y 297 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7221 (mt-10) REVERT: Y 415 ASN cc_start: 0.8239 (t0) cc_final: 0.7589 (t0) REVERT: Y 417 THR cc_start: 0.8633 (p) cc_final: 0.8274 (t) REVERT: Y 458 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8296 (pt) outliers start: 114 outliers final: 87 residues processed: 937 average time/residue: 0.4799 time to fit residues: 678.7271 Evaluate side-chains 976 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 878 time to evaluate : 3.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1001 ILE Chi-restraints excluded: chain Q residue 1168 LYS Chi-restraints excluded: chain Q residue 1242 ILE Chi-restraints excluded: chain Q residue 1267 ASP Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain Q residue 1301 LEU Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 261 ILE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 595 LEU Chi-restraints excluded: chain R residue 612 MET Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 617 GLU Chi-restraints excluded: chain R residue 653 GLN Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain T residue 314 ASN Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 86 MET Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 222 VAL Chi-restraints excluded: chain U residue 235 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 349 ASP Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain U residue 458 ILE Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 225 GLU Chi-restraints excluded: chain V residue 243 ILE Chi-restraints excluded: chain V residue 274 LYS Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 317 ASP Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 350 THR Chi-restraints excluded: chain V residue 373 LEU Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 266 ARG Chi-restraints excluded: chain W residue 315 ASP Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 368 LEU Chi-restraints excluded: chain W residue 402 LEU Chi-restraints excluded: chain W residue 429 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 226 THR Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 367 LEU Chi-restraints excluded: chain X residue 389 THR Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 115 GLU Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 357 LYS Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 458 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 317 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 309 optimal weight: 0.7980 chunk 319 optimal weight: 0.7980 chunk 191 optimal weight: 0.0970 chunk 143 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 335 optimal weight: 1.9990 chunk 209 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1316 HIS ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS R 146 GLN R 666 ASN ** R 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 ASN T 256 ASN T 417 GLN T 437 ASN U 272 GLN ** V 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 325 ASN V 417 GLN W 173 ASN Y 401 ASN Y 408 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.121736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.100855 restraints weight = 46167.668| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.28 r_work: 0.3182 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29103 Z= 0.147 Angle : 0.616 11.211 39373 Z= 0.303 Chirality : 0.044 0.188 4620 Planarity : 0.004 0.077 5040 Dihedral : 6.592 121.225 4005 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.42 % Allowed : 24.93 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3618 helix: 1.08 (0.14), residues: 1501 sheet: 0.65 (0.20), residues: 655 loop : -0.88 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q1361 HIS 0.020 0.001 HIS R 121 PHE 0.022 0.001 PHE R 691 TYR 0.025 0.002 TYR X 323 ARG 0.018 0.000 ARG V 371 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 1074) hydrogen bonds : angle 3.98255 ( 3132) covalent geometry : bond 0.00348 (29102) covalent geometry : angle 0.61638 (39373) Misc. bond : bond 0.01048 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 884 time to evaluate : 3.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1007 PHE cc_start: 0.7819 (m-80) cc_final: 0.7566 (m-80) REVERT: Q 1150 LYS cc_start: 0.8621 (tppt) cc_final: 0.8340 (tppt) REVERT: Q 1189 SER cc_start: 0.8575 (t) cc_final: 0.8312 (p) REVERT: Q 1195 LYS cc_start: 0.7915 (pptt) cc_final: 0.7516 (pptt) REVERT: Q 1208 ARG cc_start: 0.8317 (ttm170) cc_final: 0.7884 (ptm160) REVERT: Q 1255 TYR cc_start: 0.8690 (t80) cc_final: 0.8399 (t80) REVERT: Q 1287 SER cc_start: 0.8809 (m) cc_final: 0.8432 (t) REVERT: Q 1327 MET cc_start: 0.5869 (mmm) cc_final: 0.5346 (mmm) REVERT: Q 1328 MET cc_start: 0.7257 (tpt) cc_final: 0.6950 (tpt) REVERT: Q 1331 MET cc_start: 0.8330 (tpp) cc_final: 0.7707 (mpp) REVERT: Q 1432 MET cc_start: 0.5451 (tpp) cc_final: 0.5025 (tpp) REVERT: R 19 PRO cc_start: 0.8575 (Cg_exo) cc_final: 0.8045 (Cg_endo) REVERT: R 93 ARG cc_start: 0.8612 (tmm-80) cc_final: 0.8183 (ttp80) REVERT: R 121 HIS cc_start: 0.7795 (OUTLIER) cc_final: 0.7311 (t-90) REVERT: R 242 GLN cc_start: 0.8203 (mt0) cc_final: 0.7903 (mt0) REVERT: R 260 ASP cc_start: 0.8286 (m-30) cc_final: 0.8006 (m-30) REVERT: R 262 GLU cc_start: 0.8030 (mp0) cc_final: 0.7470 (mp0) REVERT: R 269 ASN cc_start: 0.7410 (t0) cc_final: 0.6987 (t0) REVERT: R 608 GLU cc_start: 0.8159 (tt0) cc_final: 0.7259 (tt0) REVERT: R 612 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7475 (mpp) REVERT: R 677 VAL cc_start: 0.8881 (t) cc_final: 0.8571 (m) REVERT: R 712 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7622 (mtpp) REVERT: R 723 GLN cc_start: 0.7067 (mp10) cc_final: 0.6500 (mp10) REVERT: R 724 TYR cc_start: 0.7784 (t80) cc_final: 0.7274 (t80) REVERT: R 736 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7328 (tm-30) REVERT: T 117 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7900 (mttt) REVERT: T 122 MET cc_start: 0.8715 (tpt) cc_final: 0.8447 (mmm) REVERT: T 417 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7763 (mt0) REVERT: T 430 ASN cc_start: 0.8506 (p0) cc_final: 0.8291 (p0) REVERT: U 105 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7753 (mt-10) REVERT: U 115 GLU cc_start: 0.8457 (tp30) cc_final: 0.8158 (tp30) REVERT: U 131 GLU cc_start: 0.7503 (pt0) cc_final: 0.7273 (pt0) REVERT: U 144 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6415 (mp10) REVERT: U 157 LYS cc_start: 0.8446 (mttt) cc_final: 0.7867 (mtpt) REVERT: U 170 GLU cc_start: 0.8060 (tp30) cc_final: 0.7786 (tp30) REVERT: U 193 ASP cc_start: 0.8147 (t0) cc_final: 0.7823 (t0) REVERT: U 233 LYS cc_start: 0.7883 (mmmt) cc_final: 0.7597 (mmmt) REVERT: U 264 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7470 (tt0) REVERT: U 279 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8193 (pt0) REVERT: U 281 LYS cc_start: 0.8954 (ttmm) cc_final: 0.8631 (tttp) REVERT: U 282 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7722 (mt-10) REVERT: U 283 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7645 (mt-10) REVERT: U 300 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.8032 (mmm) REVERT: U 316 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7359 (mm-30) REVERT: U 374 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7760 (tm-30) REVERT: U 413 ARG cc_start: 0.8263 (mtm110) cc_final: 0.8046 (ptm-80) REVERT: U 437 VAL cc_start: 0.8908 (m) cc_final: 0.8700 (p) REVERT: U 458 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8255 (pt) REVERT: V 42 LYS cc_start: 0.8064 (mtmm) cc_final: 0.7484 (tttt) REVERT: V 69 LYS cc_start: 0.8508 (mttm) cc_final: 0.8247 (mtpp) REVERT: V 99 LYS cc_start: 0.8623 (mtpt) cc_final: 0.8387 (mtpt) REVERT: V 135 GLU cc_start: 0.7364 (tt0) cc_final: 0.7102 (tt0) REVERT: V 144 VAL cc_start: 0.8612 (t) cc_final: 0.8265 (m) REVERT: V 153 GLU cc_start: 0.7899 (pm20) cc_final: 0.7681 (pm20) REVERT: V 177 LYS cc_start: 0.8921 (ttpp) cc_final: 0.8464 (ttpp) REVERT: V 242 GLU cc_start: 0.8263 (mp0) cc_final: 0.7696 (mp0) REVERT: V 264 ASP cc_start: 0.7798 (p0) cc_final: 0.7570 (p0) REVERT: V 294 LYS cc_start: 0.8738 (tppt) cc_final: 0.8517 (tppt) REVERT: V 297 ASP cc_start: 0.8342 (t0) cc_final: 0.8020 (t0) REVERT: V 355 SER cc_start: 0.8333 (m) cc_final: 0.8130 (t) REVERT: V 429 SER cc_start: 0.9052 (m) cc_final: 0.8851 (t) REVERT: V 454 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8533 (ttmm) REVERT: W 38 ARG cc_start: 0.8792 (mtm-85) cc_final: 0.8581 (mtt90) REVERT: W 167 THR cc_start: 0.8811 (p) cc_final: 0.8540 (t) REVERT: W 378 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7485 (tm-30) REVERT: W 388 THR cc_start: 0.8636 (m) cc_final: 0.8343 (p) REVERT: W 395 SER cc_start: 0.8637 (t) cc_final: 0.8318 (m) REVERT: W 413 ARG cc_start: 0.8481 (mtp180) cc_final: 0.8154 (mtm180) REVERT: W 443 ASN cc_start: 0.7896 (m110) cc_final: 0.7664 (m-40) REVERT: W 449 ASP cc_start: 0.7961 (t70) cc_final: 0.7692 (p0) REVERT: X 138 GLU cc_start: 0.6914 (tm-30) cc_final: 0.6462 (tm-30) REVERT: X 143 GLU cc_start: 0.8208 (tt0) cc_final: 0.7984 (tt0) REVERT: X 192 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7576 (mt-10) REVERT: X 210 LYS cc_start: 0.8203 (ptmt) cc_final: 0.7886 (ptmt) REVERT: X 211 ARG cc_start: 0.8340 (mtp-110) cc_final: 0.7752 (mtp180) REVERT: X 226 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8047 (p) REVERT: X 228 GLU cc_start: 0.7917 (pt0) cc_final: 0.7531 (pt0) REVERT: X 276 LYS cc_start: 0.7991 (tmtt) cc_final: 0.7699 (tmtt) REVERT: X 290 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7996 (mtmt) REVERT: X 367 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8594 (pp) REVERT: X 385 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8272 (tt0) REVERT: X 428 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8470 (t) REVERT: Y 115 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7405 (tm-30) REVERT: Y 210 ARG cc_start: 0.8237 (mmm160) cc_final: 0.7929 (mmm160) REVERT: Y 248 ASN cc_start: 0.8722 (m-40) cc_final: 0.8443 (m-40) REVERT: Y 297 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7212 (mt-10) REVERT: Y 415 ASN cc_start: 0.8222 (t0) cc_final: 0.7526 (t0) REVERT: Y 417 THR cc_start: 0.8604 (p) cc_final: 0.8232 (t) REVERT: Y 458 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8292 (pt) outliers start: 108 outliers final: 82 residues processed: 932 average time/residue: 0.4684 time to fit residues: 658.1515 Evaluate side-chains 970 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 874 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1001 ILE Chi-restraints excluded: chain Q residue 1168 LYS Chi-restraints excluded: chain Q residue 1242 ILE Chi-restraints excluded: chain Q residue 1267 ASP Chi-restraints excluded: chain Q residue 1273 LEU Chi-restraints excluded: chain Q residue 1301 LEU Chi-restraints excluded: chain R residue 24 THR Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 261 ILE Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 595 LEU Chi-restraints excluded: chain R residue 612 MET Chi-restraints excluded: chain R residue 615 ASN Chi-restraints excluded: chain R residue 617 GLU Chi-restraints excluded: chain R residue 653 GLN Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 117 LYS Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain T residue 314 ASN Chi-restraints excluded: chain T residue 417 GLN Chi-restraints excluded: chain T residue 448 ASP Chi-restraints excluded: chain U residue 56 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 86 MET Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 222 VAL Chi-restraints excluded: chain U residue 235 VAL Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain U residue 422 ASP Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain U residue 458 ILE Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 225 GLU Chi-restraints excluded: chain V residue 243 ILE Chi-restraints excluded: chain V residue 274 LYS Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 317 ASP Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 350 THR Chi-restraints excluded: chain V residue 373 LEU Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 212 TYR Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 261 ASP Chi-restraints excluded: chain W residue 266 ARG Chi-restraints excluded: chain W residue 315 ASP Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 355 THR Chi-restraints excluded: chain W residue 368 LEU Chi-restraints excluded: chain W residue 402 LEU Chi-restraints excluded: chain W residue 429 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 226 THR Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 367 LEU Chi-restraints excluded: chain X residue 389 THR Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain Y residue 110 GLU Chi-restraints excluded: chain Y residue 115 GLU Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 357 LYS Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 458 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 200 optimal weight: 0.9980 chunk 228 optimal weight: 0.0060 chunk 81 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 159 optimal weight: 0.0970 chunk 286 optimal weight: 0.2980 chunk 107 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1316 HIS R 107 ASN R 121 HIS R 146 GLN R 666 ASN ** R 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 256 ASN T 417 GLN T 437 ASN U 272 GLN ** V 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 417 GLN W 173 ASN Y 62 GLN Y 63 ASN Y 443 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.122800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.101944 restraints weight = 45818.749| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.27 r_work: 0.3209 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29103 Z= 0.112 Angle : 0.599 10.943 39373 Z= 0.293 Chirality : 0.043 0.189 4620 Planarity : 0.004 0.071 5040 Dihedral : 6.444 117.874 4005 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.01 % Allowed : 25.37 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3618 helix: 1.15 (0.14), residues: 1501 sheet: 0.70 (0.20), residues: 650 loop : -0.82 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q1361 HIS 0.020 0.001 HIS R 121 PHE 0.022 0.001 PHE R 691 TYR 0.019 0.001 TYR U 427 ARG 0.017 0.000 ARG R 97 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 1074) hydrogen bonds : angle 3.90466 ( 3132) covalent geometry : bond 0.00261 (29102) covalent geometry : angle 0.59916 (39373) Misc. bond : bond 0.00917 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22304.51 seconds wall clock time: 385 minutes 34.17 seconds (23134.17 seconds total)