Starting phenix.real_space_refine on Mon Aug 25 14:17:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8etw_28601/08_2025/8etw_28601_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8etw_28601/08_2025/8etw_28601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8etw_28601/08_2025/8etw_28601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8etw_28601/08_2025/8etw_28601.map" model { file = "/net/cci-nas-00/data/ceres_data/8etw_28601/08_2025/8etw_28601_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8etw_28601/08_2025/8etw_28601_neut.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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 18039 2.51 5 N 4942 2.21 5 O 5578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28666 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: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3350 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 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: 5.77, per 1000 atoms: 0.20 Number of scatterers: 28666 At special positions: 0 Unit cell: (128.59, 158.65, 197.06, 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 5578 8.00 N 4942 7.00 C 18039 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.4 microseconds 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: 151 helices and 33 sheets defined 44.2% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'Q' and resid 957 through 971 removed outlier: 3.913A pdb=" N ILE Q 971 " --> pdb=" O LEU Q 967 " (cutoff:3.500A) Processing helix chain 'Q' and resid 974 through 985 removed outlier: 3.811A pdb=" N ASP Q 985 " --> pdb=" O ALA Q 981 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1000 through 1013 removed outlier: 3.960A pdb=" N GLN Q1006 " --> pdb=" O ASN Q1002 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE Q1007 " --> pdb=" O ALA Q1003 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1013 through 1018 removed outlier: 4.388A pdb=" N PHE Q1017 " --> pdb=" O HIS Q1013 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1086 through 1094 removed outlier: 3.915A 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 1145 Processing helix chain 'Q' and resid 1147 through 1154 Processing helix chain 'Q' and resid 1169 through 1178 removed outlier: 3.605A pdb=" N VAL Q1177 " --> pdb=" O GLU Q1173 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR Q1178 " --> pdb=" O LEU Q1174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1185 through 1191 Processing helix chain 'Q' and resid 1192 through 1201 removed outlier: 3.527A pdb=" N HIS Q1196 " --> pdb=" O ASN Q1192 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU Q1201 " --> pdb=" O ALA Q1197 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1226 through 1238 removed outlier: 3.867A 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 1292 through 1297 Processing helix chain 'Q' and resid 1298 through 1315 removed outlier: 3.827A pdb=" N VAL Q1309 " --> pdb=" O ASP Q1305 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS Q1310 " --> pdb=" O GLU Q1306 " (cutoff:3.500A) removed outlier: 3.618A 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: 3.701A pdb=" N GLN Q1403 " --> pdb=" O THR Q1399 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1427 through 1432 removed outlier: 3.630A pdb=" N ARG Q1431 " --> pdb=" O THR Q1427 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 34 Processing helix chain 'R' and resid 84 through 87 Processing helix chain 'R' and resid 89 through 95 removed outlier: 3.509A pdb=" N GLN R 95 " --> pdb=" O ALA R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 121 Processing helix chain 'R' and resid 143 through 158 Processing helix chain 'R' and resid 167 through 177 Processing helix chain 'R' and resid 215 through 231 Processing helix chain 'R' and resid 239 through 250 removed outlier: 3.761A pdb=" N TYR R 243 " --> pdb=" O SER R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 262 removed outlier: 3.565A pdb=" N ASP R 260 " --> pdb=" O ASN R 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE R 261 " --> pdb=" O TYR R 257 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU R 262 " --> pdb=" O ASP R 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 256 through 262' Processing helix chain 'R' and resid 266 through 271 Processing helix chain 'R' and resid 585 through 588 Processing helix chain 'R' and resid 589 through 596 Processing helix chain 'R' and resid 606 through 609 Processing helix chain 'R' and resid 616 through 621 Processing helix chain 'R' and resid 622 through 626 removed outlier: 3.845A pdb=" N ILE R 625 " --> pdb=" O PRO R 622 " (cutoff:3.500A) Processing helix chain 'R' and resid 637 through 648 Processing helix chain 'R' and resid 658 through 666 Processing helix chain 'R' and resid 672 through 677 removed outlier: 3.571A pdb=" N LYS R 676 " --> pdb=" O GLY R 673 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL R 677 " --> pdb=" O ASN R 674 " (cutoff:3.500A) 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 29 through 40 removed outlier: 4.323A pdb=" N LEU S 33 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG S 34 " --> pdb=" O LEU S 30 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL S 36 " --> pdb=" O PHE S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 83 removed outlier: 3.613A pdb=" N LEU S 66 " --> pdb=" O SER S 62 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE S 67 " --> pdb=" O ALA S 63 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER S 68 " --> pdb=" O ARG S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 104 removed outlier: 3.892A pdb=" N GLU S 104 " --> pdb=" O TYR S 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'S' and resid 150 through 157 removed outlier: 3.762A pdb=" N GLU S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 68 removed outlier: 3.526A pdb=" N ARG T 55 " --> pdb=" O GLN T 51 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS T 68 " --> pdb=" O LEU T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 97 Processing helix chain 'T' and resid 108 through 111 removed outlier: 3.600A 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 256 Processing helix chain 'T' and resid 281 through 298 removed outlier: 3.519A pdb=" N ARG T 285 " --> pdb=" O THR T 281 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN T 298 " --> pdb=" O LYS T 294 " (cutoff:3.500A) Processing helix chain 'T' and resid 312 through 316 Processing helix chain 'T' and resid 317 through 328 removed outlier: 3.827A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) Processing helix chain 'T' and resid 360 through 365 removed outlier: 3.661A 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: 3.885A pdb=" N ALA T 415 " --> pdb=" O SER T 411 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU T 416 " --> pdb=" O LEU T 412 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ALA T 420 " --> pdb=" O LEU T 416 " (cutoff:3.500A) Proline residue: T 421 - end of helix removed outlier: 3.640A 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 Processing helix chain 'U' and resid 81 through 93 removed outlier: 3.533A 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: 4.029A pdb=" N ARG U 270 " --> pdb=" O ARG U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 298 through 301 removed outlier: 3.509A 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 313 removed outlier: 3.779A pdb=" N ARG U 311 " --> pdb=" O SER U 307 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU U 313 " --> pdb=" O ILE U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 340 through 343 Processing helix chain 'U' and resid 344 through 350 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: 3.617A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL U 405 " --> pdb=" O ASN U 401 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN U 407 " --> pdb=" O ILE U 403 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE U 409 " --> pdb=" O VAL U 405 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG U 413 " --> pdb=" O ILE U 409 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 Processing helix chain 'U' and resid 432 through 443 Processing helix chain 'U' and resid 444 through 447 removed outlier: 3.630A pdb=" N TYR U 447 " --> pdb=" O GLU U 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 444 through 447' Processing helix chain 'V' and resid 51 through 68 removed outlier: 3.922A pdb=" N LYS V 68 " --> pdb=" O LEU V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 97 removed outlier: 3.587A pdb=" N LEU V 88 " --> pdb=" O GLY V 84 " (cutoff:3.500A) Processing helix chain 'V' and resid 108 through 111 removed outlier: 3.690A 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: 3.694A 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: 3.854A pdb=" N GLN V 271 " --> pdb=" O SER V 267 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 298 removed outlier: 3.618A 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: 3.777A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) Processing helix chain 'V' and resid 356 through 359 Processing helix chain 'V' and resid 360 through 365 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 418 Processing helix chain 'V' and resid 418 through 428 Processing helix chain 'V' and resid 435 through 446 Processing helix chain 'V' and resid 448 through 458 Processing helix chain 'W' and resid 47 through 64 removed outlier: 3.596A pdb=" N GLY W 64 " --> pdb=" O MET W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 93 removed outlier: 3.915A pdb=" N GLY W 93 " --> pdb=" O SER W 89 " (cutoff:3.500A) 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: 4.222A pdb=" N ARG W 250 " --> pdb=" O VAL W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 252 through 260 removed outlier: 3.603A pdb=" N ALA W 256 " --> pdb=" O GLN W 252 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE W 258 " --> pdb=" O PHE W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 283 removed outlier: 3.761A pdb=" N ARG W 270 " --> pdb=" O ARG W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 313 removed outlier: 3.936A 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: 3.643A pdb=" N ARG W 350 " --> pdb=" O ASP W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 375 removed outlier: 3.653A pdb=" N ILE W 364 " --> pdb=" O ASN W 360 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 394 Processing helix chain 'W' and resid 395 through 413 removed outlier: 3.790A pdb=" N SER W 399 " --> pdb=" O SER W 395 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG W 413 " --> pdb=" O ILE W 409 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 430 removed outlier: 3.580A pdb=" N VAL W 423 " --> pdb=" O GLU W 419 " (cutoff:3.500A) Processing helix chain 'W' and resid 432 through 442 removed outlier: 3.518A pdb=" N SER W 436 " --> pdb=" O ASP W 432 " (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: 3.603A 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 182 through 184 No H-bonds generated for 'chain 'X' and resid 182 through 184' Processing helix chain 'X' and resid 185 through 193 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: 3.688A pdb=" N ARG X 258 " --> pdb=" O VAL X 254 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 272 removed outlier: 3.608A pdb=" N MET X 268 " --> pdb=" O ASP X 264 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU X 272 " --> pdb=" O MET X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 298 removed outlier: 3.621A pdb=" N ARG X 285 " --> pdb=" O THR X 281 " (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: 3.716A 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 47 through 64 Processing helix chain 'Y' and resid 80 through 92 Processing helix chain 'Y' and resid 104 through 107 removed outlier: 3.966A pdb=" N PHE Y 107 " --> pdb=" O SER Y 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 104 through 107' Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'Y' and resid 172 through 181 removed outlier: 3.829A pdb=" N LYS Y 181 " --> pdb=" O ASP Y 177 " (cutoff:3.500A) 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: 3.880A pdb=" N ARG Y 270 " --> pdb=" O ARG Y 266 " (cutoff:3.500A) Processing helix chain 'Y' and resid 302 through 313 removed outlier: 3.637A pdb=" N LEU Y 313 " --> pdb=" O ILE Y 309 " (cutoff:3.500A) Processing helix chain 'Y' and resid 344 through 350 removed outlier: 3.581A pdb=" N ARG Y 350 " --> pdb=" O ASP Y 346 " (cutoff:3.500A) 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: 4.097A pdb=" N SER Y 399 " --> pdb=" O SER Y 395 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG Y 413 " --> pdb=" O ILE Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 Processing helix chain 'Y' and resid 432 through 442 removed outlier: 3.602A pdb=" N SER Y 436 " --> pdb=" O ASP Y 432 " (cutoff:3.500A) Processing helix chain 'Y' and resid 443 through 447 Processing sheet with id=AA1, first strand: chain 'Q' and resid 949 through 954 removed outlier: 6.931A pdb=" N ILE Q 950 " --> pdb=" O ARG Q1421 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU Q1423 " --> pdb=" O ILE Q 950 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL Q 952 " --> pdb=" O LEU Q1423 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU Q1319 " --> pdb=" O ILE Q1390 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE Q1343 " --> pdb=" O LEU Q1371 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N SER Q1373 " --> pdb=" O ILE Q1343 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 1026 through 1027 removed outlier: 6.064A 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: 3.692A 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: 6.443A pdb=" N VAL V 230 " --> pdb=" O VAL V 212 " (cutoff:3.500A) removed outlier: 6.069A 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 Processing sheet with id=AA5, first strand: chain 'R' and resid 14 through 15 removed outlier: 6.700A pdb=" N VAL R 14 " --> pdb=" O GLU R 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 61 through 64 removed outlier: 3.865A pdb=" N THR R 137 " --> pdb=" O ILE R 42 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N PHE R 44 " --> pdb=" O THR R 137 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N GLY R 166 " --> pdb=" O ILE R 134 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU R 136 " --> pdb=" O GLY R 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 67 through 71 Processing sheet with id=AA8, first strand: chain 'R' and resid 100 through 101 removed outlier: 3.993A pdb=" N PHE R 104 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 162 through 163 Processing sheet with id=AB1, 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=AB2, first strand: chain 'S' and resid 125 through 126 removed outlier: 3.504A pdb=" N TYR S 125 " --> pdb=" O TYR S 134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 44 through 45 Processing sheet with id=AB4, first strand: chain 'T' and resid 102 through 106 removed outlier: 6.346A pdb=" N CYS T 103 " --> pdb=" O PHE T 309 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP T 311 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU T 105 " --> pdb=" O ASP T 311 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE T 75 " --> pdb=" O LEU T 338 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N SER T 340 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU T 77 " --> pdb=" O SER T 340 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ALA T 74 " --> pdb=" O LEU T 368 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N VAL T 370 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU T 76 " --> pdb=" O VAL T 370 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 129 through 151 removed outlier: 6.337A pdb=" N GLY T 169 " --> pdb=" O THR T 145 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU T 147 " --> pdb=" O ILE T 167 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE T 167 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N HIS T 165 " --> pdb=" O PRO T 149 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASP T 151 " --> pdb=" O ILE T 163 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE T 163 " --> pdb=" O ASP T 151 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY T 175 " --> pdb=" O SER T 172 " (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: 6.069A pdb=" N VAL T 230 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG T 214 " --> pdb=" O VAL T 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'T' and resid 344 through 346 Processing sheet with id=AB7, first strand: chain 'U' and resid 40 through 41 Processing sheet with id=AB8, first strand: chain 'U' and resid 98 through 102 removed outlier: 6.433A pdb=" N THR U 99 " --> pdb=" O PHE U 294 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ASP U 296 " --> pdb=" O THR U 99 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE U 101 " --> pdb=" O ASP U 296 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU U 293 " --> pdb=" O MET U 322 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA U 324 " --> pdb=" O LEU U 293 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE U 295 " --> pdb=" O ALA U 324 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 125 through 147 removed outlier: 6.689A pdb=" N THR U 159 " --> pdb=" O VAL U 141 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE U 143 " --> pdb=" O LYS U 157 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS U 157 " --> pdb=" O ILE U 143 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE U 145 " --> pdb=" O GLN U 155 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN U 155 " --> pdb=" O ILE U 145 " (cutoff:3.500A) removed outlier: 4.355A 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=AC1, first strand: chain 'U' and resid 330 through 331 Processing sheet with id=AC2, first strand: chain 'V' and resid 44 through 45 Processing sheet with id=AC3, first strand: chain 'V' and resid 102 through 106 removed outlier: 6.346A pdb=" N CYS V 103 " --> pdb=" O PHE V 309 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASP V 311 " --> pdb=" O CYS V 103 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU V 105 " --> pdb=" O ASP V 311 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU V 308 " --> pdb=" O VAL V 337 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ALA V 339 " --> pdb=" O LEU V 308 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE V 310 " --> pdb=" O ALA V 339 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY V 79 " --> pdb=" O SER V 340 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA V 74 " --> pdb=" O LEU V 368 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL V 370 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU V 76 " --> pdb=" O VAL V 370 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR V 372 " --> pdb=" O LEU V 76 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA V 78 " --> pdb=" O THR V 372 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 345 through 346 Processing sheet with id=AC5, first strand: chain 'W' and resid 40 through 41 Processing sheet with id=AC6, first strand: chain 'W' and resid 98 through 102 removed outlier: 6.452A pdb=" N THR W 99 " --> pdb=" O PHE W 294 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASP W 296 " --> pdb=" O THR W 99 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE W 101 " --> pdb=" O ASP W 296 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU W 293 " --> pdb=" O MET W 322 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ALA W 324 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE W 295 " --> pdb=" O ALA W 324 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 125 through 147 removed outlier: 5.285A pdb=" N VAL W 140 " --> pdb=" O LYS W 161 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LYS W 161 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 3.817A 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: 3.504A pdb=" N VAL X 166 " --> pdb=" O LEU X 181 " (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 207 through 215 removed outlier: 6.471A pdb=" N VAL X 230 " --> pdb=" O VAL X 212 " (cutoff:3.500A) removed outlier: 5.533A 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=AC8, first strand: chain 'W' and resid 330 through 331 Processing sheet with id=AC9, first strand: chain 'X' and resid 44 through 45 removed outlier: 3.503A pdb=" N GLU X 45 " --> pdb=" O PHE X 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 102 through 106 removed outlier: 3.755A pdb=" N SER X 340 " --> pdb=" O LEU X 77 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY X 79 " --> pdb=" O SER X 340 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 344 through 346 Processing sheet with id=AD3, first strand: chain 'Y' and resid 40 through 41 Processing sheet with id=AD4, first strand: chain 'Y' and resid 98 through 102 removed outlier: 6.349A pdb=" N THR Y 99 " --> pdb=" O PHE Y 294 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP Y 296 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE Y 101 " --> pdb=" O ASP Y 296 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ALA Y 70 " --> pdb=" O ILE Y 352 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Y' and resid 125 through 147 removed outlier: 6.890A pdb=" N THR Y 159 " --> pdb=" O VAL Y 141 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE Y 143 " --> pdb=" O LYS Y 157 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS Y 157 " --> pdb=" O ILE Y 143 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE Y 145 " --> pdb=" O GLN Y 155 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLN Y 155 " --> pdb=" O ILE Y 145 " (cutoff:3.500A) removed outlier: 3.641A 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: 5.727A pdb=" N VAL Y 222 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ARG Y 204 " --> pdb=" O VAL Y 222 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 329 through 331 1092 hydrogen bonds defined for protein. 3174 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: 5.00 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9096 1.34 - 1.46: 5669 1.46 - 1.58: 14147 1.58 - 1.71: 20 1.71 - 1.83: 166 Bond restraints: 29098 Sorted by residual: bond pdb=" CB PRO R 27 " pdb=" CG PRO R 27 " ideal model delta sigma weight residual 1.492 1.656 -0.164 5.00e-02 4.00e+02 1.08e+01 bond pdb=" N GLU X 225 " pdb=" CA GLU X 225 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.16e-02 7.43e+03 8.54e+00 bond pdb=" N SER V 340 " pdb=" CA SER V 340 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.29e-02 6.01e+03 7.11e+00 bond pdb=" N ARG V 342 " pdb=" CA ARG V 342 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.21e-02 6.83e+03 6.64e+00 bond pdb=" N GLU R 617 " pdb=" CA GLU R 617 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.25e-02 6.40e+03 6.35e+00 ... (remaining 29093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 39062 4.07 - 8.14: 276 8.14 - 12.22: 22 12.22 - 16.29: 5 16.29 - 20.36: 3 Bond angle restraints: 39368 Sorted by residual: angle pdb=" CA PRO R 27 " pdb=" N PRO R 27 " pdb=" CD PRO R 27 " ideal model delta sigma weight residual 112.00 97.75 14.25 1.40e+00 5.10e-01 1.04e+02 angle pdb=" N MET V 344 " pdb=" CA MET V 344 " pdb=" C MET V 344 " ideal model delta sigma weight residual 107.28 91.80 15.48 1.75e+00 3.27e-01 7.83e+01 angle pdb=" N GLY V 343 " pdb=" CA GLY V 343 " pdb=" C GLY V 343 " ideal model delta sigma weight residual 113.18 133.54 -20.36 2.37e+00 1.78e-01 7.38e+01 angle pdb=" N MET V 344 " pdb=" CA MET V 344 " pdb=" CB MET V 344 " ideal model delta sigma weight residual 111.74 125.94 -14.20 1.69e+00 3.50e-01 7.06e+01 angle pdb=" C LEU U 19 " pdb=" N ILE U 20 " pdb=" CA ILE U 20 " ideal model delta sigma weight residual 121.97 133.82 -11.85 1.80e+00 3.09e-01 4.33e+01 ... (remaining 39363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.07: 17000 33.07 - 66.15: 813 66.15 - 99.22: 53 99.22 - 132.29: 6 132.29 - 165.37: 5 Dihedral angle restraints: 17877 sinusoidal: 7315 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 300.00 134.64 165.37 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" O1B ADP T 501 " pdb=" O3A ADP T 501 " pdb=" PB ADP T 501 " pdb=" PA ADP T 501 " ideal model delta sinusoidal sigma weight residual 300.00 140.64 159.36 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C5' ADP T 501 " pdb=" O5' ADP T 501 " pdb=" PA ADP T 501 " pdb=" O2A ADP T 501 " ideal model delta sinusoidal sigma weight residual 300.00 150.00 150.00 1 2.00e+01 2.50e-03 4.48e+01 ... (remaining 17874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3932 0.075 - 0.149: 637 0.149 - 0.224: 44 0.224 - 0.298: 4 0.298 - 0.373: 3 Chirality restraints: 4620 Sorted by residual: chirality pdb=" CG LEU Q 963 " pdb=" CB LEU Q 963 " pdb=" CD1 LEU Q 963 " pdb=" CD2 LEU Q 963 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CB ILE Y 160 " pdb=" CA ILE Y 160 " pdb=" CG1 ILE Y 160 " pdb=" CG2 ILE Y 160 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CB THR U 40 " pdb=" CA THR U 40 " pdb=" OG1 THR U 40 " pdb=" CG2 THR U 40 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 4617 not shown) Planarity restraints: 5039 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 58 " -0.089 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO R 59 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO R 59 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO R 59 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 599 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO R 600 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO R 600 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO R 600 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU U 182 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.56e+01 pdb=" C GLU U 182 " 0.068 2.00e-02 2.50e+03 pdb=" O GLU U 182 " -0.026 2.00e-02 2.50e+03 pdb=" N LYS U 183 " -0.022 2.00e-02 2.50e+03 ... (remaining 5036 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 4 2.13 - 2.82: 8329 2.82 - 3.51: 36317 3.51 - 4.21: 65485 4.21 - 4.90: 115671 Nonbonded interactions: 225806 Sorted by model distance: nonbonded pdb=" OH TYR W 212 " pdb=" OD1 ASP X 182 " model vdw 1.435 3.040 nonbonded pdb=" CD2 LEU R 614 " pdb=" OE2 GLU R 617 " model vdw 1.666 3.460 nonbonded pdb=" NZ LYS Y 113 " pdb=" OD2 ASP Y 302 " model vdw 1.725 3.120 nonbonded pdb=" OH TYR W 212 " pdb=" CG ASP X 182 " model vdw 2.070 3.270 nonbonded pdb=" OE2 GLU R 733 " pdb=" OH TYR R 741 " model vdw 2.134 3.040 ... (remaining 225801 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 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 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 501)) } ncs_group { reference = (chain 'U' and (resid 18 through 459 or resid 501)) selection = (chain 'W' and (resid 18 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 210 or resid 221 through 501)) selection = (chain 'Y' and (resid 18 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 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: 10.510 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: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.410 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 0.006 0.458 29100 Z= 0.353 Angle : 0.910 20.362 39368 Z= 0.479 Chirality : 0.054 0.373 4620 Planarity : 0.007 0.131 5039 Dihedral : 18.081 165.365 11057 Min Nonbonded Distance : 1.435 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.09 % Allowed : 28.01 % Favored : 71.90 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.12), residues: 3618 helix: -1.54 (0.11), residues: 1493 sheet: 0.58 (0.20), residues: 649 loop : -1.51 (0.14), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG S 73 TYR 0.050 0.002 TYR X 323 PHE 0.046 0.002 PHE Q1167 TRP 0.018 0.002 TRP Y 280 HIS 0.008 0.001 HIS T 250 Details of bonding type rmsd covalent geometry : bond 0.00528 (29098) covalent geometry : angle 0.90986 (39368) hydrogen bonds : bond 0.17591 ( 1092) hydrogen bonds : angle 6.24394 ( 3174) Misc. bond : bond 0.32392 ( 2) *********************** 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 860 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 857 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1122 TYR cc_start: 0.8688 (t80) cc_final: 0.8275 (t80) REVERT: R 719 ARG cc_start: 0.7512 (mpp80) cc_final: 0.7246 (mpp80) REVERT: T 268 MET cc_start: 0.7590 (mmm) cc_final: 0.7382 (mpp) REVERT: V 341 ASN cc_start: 0.7519 (p0) cc_final: 0.7058 (p0) REVERT: Y 174 LYS cc_start: 0.7712 (mttp) cc_final: 0.7503 (mmtp) REVERT: Z 311 ARG cc_start: 0.7781 (mpp80) cc_final: 0.7436 (mtt-85) outliers start: 3 outliers final: 4 residues processed: 859 average time/residue: 0.6938 time to fit residues: 681.0945 Evaluate side-chains 820 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 816 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.0020 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.0570 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.4306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1117 ASN Q1204 ASN R 146 GLN R 611 GLN R 723 GLN U 63 ASN U 274 ASN U 310 ASN U 446 GLN V 190 GLN V 205 ASN V 394 GLN X 190 GLN X 256 ASN X 325 ASN ** Y 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 252 GLN Y 310 ASN Y 441 GLN Y 443 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.131603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.111381 restraints weight = 39922.484| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.00 r_work: 0.3357 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 29100 Z= 0.128 Angle : 0.578 9.568 39368 Z= 0.289 Chirality : 0.043 0.210 4620 Planarity : 0.005 0.097 5039 Dihedral : 8.488 146.874 4010 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.83 % Allowed : 23.99 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.13), residues: 3618 helix: -0.06 (0.13), residues: 1522 sheet: 0.65 (0.20), residues: 646 loop : -1.18 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 366 TYR 0.019 0.001 TYR X 323 PHE 0.024 0.001 PHE R 691 TRP 0.011 0.001 TRP Y 280 HIS 0.003 0.001 HIS Y 237 Details of bonding type rmsd covalent geometry : bond 0.00298 (29098) covalent geometry : angle 0.57761 (39368) hydrogen bonds : bond 0.04327 ( 1092) hydrogen bonds : angle 4.25364 ( 3174) Misc. bond : bond 0.00453 ( 2) *********************** 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 1011 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 890 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1016 LEU cc_start: 0.8273 (mm) cc_final: 0.8048 (mm) REVERT: Q 1103 ASP cc_start: 0.7653 (p0) cc_final: 0.7118 (p0) REVERT: Q 1139 GLU cc_start: 0.7502 (tp30) cc_final: 0.7216 (tp30) REVERT: Q 1167 PHE cc_start: 0.7326 (m-10) cc_final: 0.7016 (m-80) REVERT: Q 1405 MET cc_start: 0.7902 (mpp) cc_final: 0.7527 (mpp) REVERT: R 101 ASP cc_start: 0.7483 (t0) cc_final: 0.7216 (t0) REVERT: R 146 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7805 (mm-40) REVERT: R 243 TYR cc_start: 0.7648 (m-10) cc_final: 0.7336 (m-10) REVERT: R 256 ASN cc_start: 0.8104 (p0) cc_final: 0.7858 (OUTLIER) REVERT: R 687 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7737 (mm-30) REVERT: S 154 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7279 (mm-30) REVERT: T 206 THR cc_start: 0.8496 (m) cc_final: 0.8268 (p) REVERT: T 241 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8304 (ttmt) REVERT: T 364 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8129 (tp) REVERT: T 431 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.8065 (mtm110) REVERT: U 62 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8379 (mt0) REVERT: U 350 ARG cc_start: 0.8535 (mtt90) cc_final: 0.8247 (mtt-85) REVERT: V 165 HIS cc_start: 0.8073 (m90) cc_final: 0.7811 (m170) REVERT: V 268 MET cc_start: 0.8125 (tpp) cc_final: 0.7879 (tpp) REVERT: V 451 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8164 (mtp180) REVERT: W 330 SER cc_start: 0.8195 (p) cc_final: 0.7984 (m) REVERT: X 37 GLU cc_start: 0.7383 (pm20) cc_final: 0.6951 (pm20) REVERT: X 94 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: X 159 TYR cc_start: 0.8375 (m-80) cc_final: 0.8169 (m-80) REVERT: X 171 LYS cc_start: 0.8802 (tttt) cc_final: 0.8580 (tttp) REVERT: X 242 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6793 (mm-30) REVERT: Y 132 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7179 (mp0) REVERT: Y 276 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7412 (ttpp) REVERT: Z 311 ARG cc_start: 0.8341 (mpp80) cc_final: 0.8099 (mtt-85) outliers start: 121 outliers final: 52 residues processed: 942 average time/residue: 0.6500 time to fit residues: 700.7764 Evaluate side-chains 908 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 850 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1143 VAL Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1328 MET Chi-restraints excluded: chain Q residue 1415 ARG Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 146 GLN Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 134 LYS Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 241 LYS Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 283 LYS Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 429 SER Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 60 MET Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 438 LYS Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 294 LYS Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 451 ARG Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 421 GLU Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 198 ASP Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 184 VAL Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 276 LYS Chi-restraints excluded: chain Y residue 331 LYS Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 428 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 259 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 340 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 320 optimal weight: 0.8980 chunk 327 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 124 optimal weight: 0.0270 chunk 244 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 56 HIS R 146 GLN R 611 GLN T 29 HIS T 256 ASN U 63 ASN U 274 ASN U 310 ASN U 407 GLN U 441 GLN V 205 ASN V 325 ASN X 256 ASN X 289 ASN X 325 ASN Y 173 ASN Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Y 443 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110040 restraints weight = 40064.007| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.86 r_work: 0.3347 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29100 Z= 0.146 Angle : 0.573 12.516 39368 Z= 0.284 Chirality : 0.044 0.143 4620 Planarity : 0.004 0.134 5039 Dihedral : 8.170 137.545 4006 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.34 % Allowed : 23.58 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.14), residues: 3618 helix: 0.50 (0.13), residues: 1527 sheet: 0.68 (0.20), residues: 641 loop : -1.09 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG Q1142 TYR 0.023 0.001 TYR X 323 PHE 0.022 0.001 PHE R 691 TRP 0.008 0.001 TRP Y 280 HIS 0.004 0.001 HIS R 56 Details of bonding type rmsd covalent geometry : bond 0.00348 (29098) covalent geometry : angle 0.57339 (39368) hydrogen bonds : bond 0.04352 ( 1092) hydrogen bonds : angle 4.04917 ( 3174) Misc. bond : bond 0.00702 ( 2) *********************** 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 1025 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 888 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1016 LEU cc_start: 0.8286 (mm) cc_final: 0.8038 (mm) REVERT: Q 1103 ASP cc_start: 0.7848 (p0) cc_final: 0.7191 (p0) REVERT: Q 1139 GLU cc_start: 0.7481 (tp30) cc_final: 0.7170 (tp30) REVERT: Q 1143 VAL cc_start: 0.7982 (OUTLIER) cc_final: 0.7347 (p) REVERT: Q 1167 PHE cc_start: 0.7438 (m-10) cc_final: 0.7040 (m-80) REVERT: Q 1184 GLU cc_start: 0.5956 (OUTLIER) cc_final: 0.5659 (pp20) REVERT: Q 1321 TYR cc_start: 0.7259 (m-80) cc_final: 0.6520 (t80) REVERT: Q 1405 MET cc_start: 0.7896 (mpp) cc_final: 0.7531 (mpp) REVERT: R 101 ASP cc_start: 0.7537 (t0) cc_final: 0.7235 (t0) REVERT: R 256 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7968 (p0) REVERT: R 687 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7717 (mm-30) REVERT: R 736 GLU cc_start: 0.7665 (tt0) cc_final: 0.7430 (tt0) REVERT: T 241 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8338 (ttmt) REVERT: T 364 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8145 (tp) REVERT: T 431 ARG cc_start: 0.8354 (mtm-85) cc_final: 0.8058 (mtm180) REVERT: U 350 ARG cc_start: 0.8533 (mtt90) cc_final: 0.8272 (mtt-85) REVERT: U 413 ARG cc_start: 0.8449 (mtp-110) cc_final: 0.8204 (mtp-110) REVERT: V 341 ASN cc_start: 0.8649 (p0) cc_final: 0.8219 (p0) REVERT: V 428 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8370 (t) REVERT: V 451 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8103 (mtp180) REVERT: W 38 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8202 (mtt180) REVERT: W 208 ARG cc_start: 0.5811 (OUTLIER) cc_final: 0.4806 (tpt-90) REVERT: W 438 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7665 (tppp) REVERT: X 37 GLU cc_start: 0.7315 (pm20) cc_final: 0.6931 (pm20) REVERT: X 56 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7715 (mt-10) REVERT: X 94 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7510 (mt0) REVERT: X 203 GLU cc_start: 0.7366 (pm20) cc_final: 0.6735 (pm20) REVERT: Y 132 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7164 (mp0) REVERT: Y 134 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7468 (mp0) REVERT: Y 276 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7449 (ttpp) REVERT: Y 300 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.6857 (mtm) REVERT: Z 311 ARG cc_start: 0.8362 (mpp80) cc_final: 0.8122 (mtt-85) outliers start: 137 outliers final: 74 residues processed: 948 average time/residue: 0.6231 time to fit residues: 677.5489 Evaluate side-chains 940 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 854 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1143 VAL Chi-restraints excluded: chain Q residue 1144 SER Chi-restraints excluded: chain Q residue 1169 THR Chi-restraints excluded: chain Q residue 1184 GLU Chi-restraints excluded: chain Q residue 1203 LEU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1328 MET Chi-restraints excluded: chain Q residue 1415 ARG Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 256 ASN Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 677 VAL Chi-restraints excluded: chain R residue 703 SER Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 134 LYS Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 150 GLU Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 241 LYS Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 282 GLU Chi-restraints excluded: chain T residue 283 LYS Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 363 LEU Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 429 SER Chi-restraints excluded: chain T residue 433 GLU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 146 GLU Chi-restraints excluded: chain V residue 190 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 385 GLU Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain V residue 451 ARG Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 208 ARG Chi-restraints excluded: chain W residue 234 THR Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 421 GLU Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 234 THR Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 276 LYS Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 331 LYS Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 432 ASP Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 237 optimal weight: 0.0470 chunk 272 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 232 optimal weight: 2.9990 chunk 277 optimal weight: 0.0270 chunk 58 optimal weight: 2.9990 chunk 279 optimal weight: 0.9980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1117 ASN R 55 ASN R 144 GLN R 224 ASN R 611 GLN T 256 ASN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 441 GLN V 205 ASN V 325 ASN X 256 ASN X 289 ASN X 325 ASN Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Y 443 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.130405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.110177 restraints weight = 39722.964| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.85 r_work: 0.3348 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29100 Z= 0.135 Angle : 0.555 9.602 39368 Z= 0.275 Chirality : 0.043 0.149 4620 Planarity : 0.004 0.089 5039 Dihedral : 8.476 177.785 4006 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.30 % Allowed : 24.62 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.14), residues: 3618 helix: 0.74 (0.14), residues: 1531 sheet: 0.74 (0.20), residues: 636 loop : -1.06 (0.15), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG Q1142 TYR 0.019 0.001 TYR V 201 PHE 0.021 0.001 PHE R 691 TRP 0.008 0.001 TRP Y 280 HIS 0.006 0.001 HIS V 165 Details of bonding type rmsd covalent geometry : bond 0.00319 (29098) covalent geometry : angle 0.55473 (39368) hydrogen bonds : bond 0.04024 ( 1092) hydrogen bonds : angle 3.96194 ( 3174) Misc. bond : bond 0.00604 ( 2) *********************** 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 998 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 862 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1000 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6356 (tp) REVERT: Q 1103 ASP cc_start: 0.7865 (p0) cc_final: 0.7278 (p0) REVERT: Q 1139 GLU cc_start: 0.7471 (tp30) cc_final: 0.7167 (tp30) REVERT: Q 1143 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7315 (p) REVERT: Q 1167 PHE cc_start: 0.7494 (m-10) cc_final: 0.7144 (m-80) REVERT: Q 1184 GLU cc_start: 0.5965 (OUTLIER) cc_final: 0.5669 (pp20) REVERT: Q 1302 ARG cc_start: 0.7300 (ttt180) cc_final: 0.7029 (ttt180) REVERT: Q 1321 TYR cc_start: 0.7257 (OUTLIER) cc_final: 0.6504 (t80) REVERT: Q 1327 MET cc_start: 0.4878 (mmm) cc_final: 0.4656 (mmm) REVERT: Q 1405 MET cc_start: 0.7893 (mpp) cc_final: 0.7559 (mtm) REVERT: R 74 LYS cc_start: 0.8326 (ttpp) cc_final: 0.8112 (tmmt) REVERT: R 242 GLN cc_start: 0.8045 (mt0) cc_final: 0.7534 (mt0) REVERT: R 687 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7694 (mm-30) REVERT: R 736 GLU cc_start: 0.7634 (tt0) cc_final: 0.7387 (tt0) REVERT: T 241 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8338 (ttmt) REVERT: T 364 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8152 (tp) REVERT: T 431 ARG cc_start: 0.8342 (mtm-85) cc_final: 0.8069 (mtm110) REVERT: U 66 ILE cc_start: 0.8435 (pp) cc_final: 0.8195 (mp) REVERT: U 228 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7364 (mm-30) REVERT: U 254 PHE cc_start: 0.8312 (p90) cc_final: 0.8111 (p90) REVERT: U 350 ARG cc_start: 0.8497 (mtt90) cc_final: 0.8251 (mtt-85) REVERT: U 413 ARG cc_start: 0.8455 (mtp-110) cc_final: 0.8243 (mtp-110) REVERT: U 422 ASP cc_start: 0.8267 (m-30) cc_final: 0.8062 (m-30) REVERT: V 319 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7704 (mm-30) REVERT: V 341 ASN cc_start: 0.8682 (p0) cc_final: 0.8207 (p0) REVERT: W 38 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8215 (mtt180) REVERT: W 220 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7170 (mpp80) REVERT: W 438 LYS cc_start: 0.8031 (ttmm) cc_final: 0.7804 (tppp) REVERT: X 37 GLU cc_start: 0.7314 (pm20) cc_final: 0.6926 (pm20) REVERT: X 94 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7470 (mt0) REVERT: X 203 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6648 (pm20) REVERT: Y 132 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7193 (mp0) REVERT: Y 134 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7465 (mp0) REVERT: Y 276 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7370 (ttpp) REVERT: Y 300 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.6941 (mtm) REVERT: Z 311 ARG cc_start: 0.8358 (mpp80) cc_final: 0.8124 (mtt-85) outliers start: 136 outliers final: 79 residues processed: 924 average time/residue: 0.6299 time to fit residues: 668.7578 Evaluate side-chains 928 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 836 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1000 LEU Chi-restraints excluded: chain Q residue 1022 VAL Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1143 VAL Chi-restraints excluded: chain Q residue 1144 SER Chi-restraints excluded: chain Q residue 1169 THR Chi-restraints excluded: chain Q residue 1184 GLU Chi-restraints excluded: chain Q residue 1203 LEU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1321 TYR Chi-restraints excluded: chain Q residue 1415 ARG Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 677 VAL Chi-restraints excluded: chain R residue 703 SER Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 134 LYS Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 241 LYS Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 282 GLU Chi-restraints excluded: chain T residue 283 LYS Chi-restraints excluded: chain T residue 300 VAL Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 402 LEU Chi-restraints excluded: chain T residue 429 SER Chi-restraints excluded: chain T residue 441 GLU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 226 GLU Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 146 GLU Chi-restraints excluded: chain V residue 190 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 294 LYS Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 234 THR Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 421 GLU Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 198 ASP Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 203 GLU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 454 LYS Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 194 LYS Chi-restraints excluded: chain Y residue 234 THR Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 276 LYS Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 331 LYS Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 432 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 250 optimal weight: 0.3980 chunk 100 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 307 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 212 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1403 GLN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 611 GLN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 441 GLN U 446 GLN V 205 ASN V 325 ASN V 394 GLN X 256 ASN X 289 ASN X 325 ASN Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Y 443 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.129961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109705 restraints weight = 39686.249| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.85 r_work: 0.3335 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29100 Z= 0.159 Angle : 0.570 9.046 39368 Z= 0.283 Chirality : 0.044 0.179 4620 Planarity : 0.004 0.076 5039 Dihedral : 8.444 179.475 4006 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.84 % Allowed : 24.05 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.14), residues: 3618 helix: 0.81 (0.14), residues: 1530 sheet: 0.75 (0.20), residues: 640 loop : -1.04 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q1142 TYR 0.026 0.002 TYR X 323 PHE 0.019 0.001 PHE R 691 TRP 0.009 0.001 TRP Y 280 HIS 0.007 0.001 HIS V 165 Details of bonding type rmsd covalent geometry : bond 0.00383 (29098) covalent geometry : angle 0.57040 (39368) hydrogen bonds : bond 0.04333 ( 1092) hydrogen bonds : angle 3.96656 ( 3174) Misc. bond : bond 0.00612 ( 2) *********************** 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 1010 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 857 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.7977 (p0) cc_final: 0.7247 (p0) REVERT: Q 1139 GLU cc_start: 0.7460 (tp30) cc_final: 0.7169 (tp30) REVERT: Q 1143 VAL cc_start: 0.7843 (OUTLIER) cc_final: 0.7262 (p) REVERT: Q 1184 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5725 (pp20) REVERT: Q 1302 ARG cc_start: 0.7285 (ttt180) cc_final: 0.7010 (ttt180) REVERT: Q 1321 TYR cc_start: 0.7331 (m-80) cc_final: 0.6553 (t80) REVERT: Q 1327 MET cc_start: 0.5057 (mmm) cc_final: 0.4721 (mmm) REVERT: Q 1405 MET cc_start: 0.7924 (mpp) cc_final: 0.7517 (mpp) REVERT: R 74 LYS cc_start: 0.8338 (ttpp) cc_final: 0.8100 (tmmt) REVERT: R 84 ASN cc_start: 0.8543 (m110) cc_final: 0.8322 (m110) REVERT: R 676 LYS cc_start: 0.6128 (ptpt) cc_final: 0.4306 (ptpp) REVERT: R 687 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7737 (mm-30) REVERT: R 736 GLU cc_start: 0.7624 (tt0) cc_final: 0.7370 (tt0) REVERT: T 241 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8342 (ttmt) REVERT: T 364 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8163 (tp) REVERT: T 431 ARG cc_start: 0.8335 (mtm-85) cc_final: 0.8013 (mtm180) REVERT: U 254 PHE cc_start: 0.8337 (p90) cc_final: 0.8135 (p90) REVERT: U 350 ARG cc_start: 0.8518 (mtt90) cc_final: 0.8249 (mtt-85) REVERT: V 319 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7690 (mm-30) REVERT: V 428 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8355 (t) REVERT: W 38 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8231 (mtt180) REVERT: W 208 ARG cc_start: 0.5842 (OUTLIER) cc_final: 0.4785 (tpt-90) REVERT: W 220 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7176 (mpp80) REVERT: W 438 LYS cc_start: 0.8086 (ttmm) cc_final: 0.7767 (tppp) REVERT: X 35 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8574 (mt) REVERT: X 37 GLU cc_start: 0.7332 (pm20) cc_final: 0.6945 (pm20) REVERT: X 94 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7499 (mt0) REVERT: X 203 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6779 (pm20) REVERT: Y 134 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7459 (mp0) REVERT: Y 276 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7996 (tttp) REVERT: Y 300 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7178 (mtm) REVERT: Z 311 ARG cc_start: 0.8378 (mpp80) cc_final: 0.8119 (mtt180) outliers start: 153 outliers final: 96 residues processed: 923 average time/residue: 0.6518 time to fit residues: 690.4964 Evaluate side-chains 955 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 845 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1143 VAL Chi-restraints excluded: chain Q residue 1144 SER Chi-restraints excluded: chain Q residue 1169 THR Chi-restraints excluded: chain Q residue 1184 GLU Chi-restraints excluded: chain Q residue 1203 LEU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1415 ARG Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 677 VAL Chi-restraints excluded: chain R residue 703 SER Chi-restraints excluded: chain R residue 723 GLN Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 241 LYS Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 282 GLU Chi-restraints excluded: chain T residue 283 LYS Chi-restraints excluded: chain T residue 300 VAL Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 363 LEU Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 402 LEU Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain T residue 429 SER Chi-restraints excluded: chain T residue 433 GLU Chi-restraints excluded: chain T residue 441 GLU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 226 GLU Chi-restraints excluded: chain U residue 283 GLU Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 146 GLU Chi-restraints excluded: chain V residue 190 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 294 LYS Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 208 ARG Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 234 THR Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 421 GLU Chi-restraints excluded: chain X residue 35 LEU Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 198 ASP Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 203 GLU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 245 GLN Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 454 LYS Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 193 ASP Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 229 LEU Chi-restraints excluded: chain Y residue 234 THR Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 276 LYS Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 304 GLU Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 331 LYS Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 432 ASP Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 98 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 297 optimal weight: 0.8980 chunk 359 optimal weight: 0.0060 chunk 321 optimal weight: 0.5980 chunk 258 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 132 ASN ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 ASN R 273 ASN R 611 GLN T 256 ASN U 62 GLN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 441 GLN V 205 ASN V 325 ASN X 190 GLN X 256 ASN X 289 ASN X 325 ASN Y 63 ASN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Y 443 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.130018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109689 restraints weight = 39689.176| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.86 r_work: 0.3338 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29100 Z= 0.147 Angle : 0.565 10.626 39368 Z= 0.280 Chirality : 0.044 0.166 4620 Planarity : 0.004 0.060 5039 Dihedral : 8.331 177.810 4006 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.68 % Allowed : 24.59 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.14), residues: 3618 helix: 0.86 (0.14), residues: 1538 sheet: 0.77 (0.20), residues: 638 loop : -1.02 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q1142 TYR 0.025 0.001 TYR R 34 PHE 0.020 0.001 PHE R 691 TRP 0.012 0.001 TRP Y 280 HIS 0.008 0.001 HIS V 27 Details of bonding type rmsd covalent geometry : bond 0.00351 (29098) covalent geometry : angle 0.56515 (39368) hydrogen bonds : bond 0.04103 ( 1092) hydrogen bonds : angle 3.93597 ( 3174) Misc. bond : bond 0.00506 ( 2) *********************** 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 1008 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 860 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.7973 (p0) cc_final: 0.7224 (p0) REVERT: Q 1139 GLU cc_start: 0.7468 (tp30) cc_final: 0.7205 (tp30) REVERT: Q 1143 VAL cc_start: 0.7791 (OUTLIER) cc_final: 0.7229 (p) REVERT: Q 1184 GLU cc_start: 0.6023 (OUTLIER) cc_final: 0.5707 (pp20) REVERT: Q 1302 ARG cc_start: 0.7305 (ttt180) cc_final: 0.7030 (ttt180) REVERT: Q 1321 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.6562 (t80) REVERT: Q 1327 MET cc_start: 0.5139 (mmm) cc_final: 0.4767 (mmm) REVERT: Q 1405 MET cc_start: 0.7986 (mpp) cc_final: 0.7535 (mpp) REVERT: R 34 TYR cc_start: 0.8206 (t80) cc_final: 0.7902 (t80) REVERT: R 74 LYS cc_start: 0.8341 (ttpp) cc_final: 0.8107 (tmmt) REVERT: R 84 ASN cc_start: 0.8519 (m110) cc_final: 0.8301 (m110) REVERT: R 676 LYS cc_start: 0.6015 (ptpt) cc_final: 0.4557 (pttt) REVERT: R 682 GLU cc_start: 0.8146 (mp0) cc_final: 0.7866 (mp0) REVERT: R 687 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7745 (mm-30) REVERT: R 736 GLU cc_start: 0.7607 (tt0) cc_final: 0.7340 (tt0) REVERT: T 241 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8348 (ttmt) REVERT: T 364 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8176 (tp) REVERT: T 456 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8414 (mp) REVERT: U 228 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7363 (mm-30) REVERT: U 254 PHE cc_start: 0.8335 (p90) cc_final: 0.8107 (p90) REVERT: U 350 ARG cc_start: 0.8488 (mtt90) cc_final: 0.8222 (mtt-85) REVERT: V 319 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7683 (mm-30) REVERT: V 325 ASN cc_start: 0.8143 (m-40) cc_final: 0.7926 (m-40) REVERT: V 428 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8354 (t) REVERT: W 38 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8267 (mtt180) REVERT: W 208 ARG cc_start: 0.5805 (OUTLIER) cc_final: 0.4772 (tpt-90) REVERT: W 220 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7155 (mpp80) REVERT: W 438 LYS cc_start: 0.8046 (ttmm) cc_final: 0.7589 (tppp) REVERT: W 442 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6754 (mt-10) REVERT: X 35 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8578 (mt) REVERT: X 37 GLU cc_start: 0.7308 (pm20) cc_final: 0.6928 (pm20) REVERT: X 94 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7478 (mt0) REVERT: X 203 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6784 (pm20) REVERT: X 344 MET cc_start: 0.8926 (mmt) cc_final: 0.8581 (mmt) REVERT: Y 23 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.6802 (p90) REVERT: Y 32 ASP cc_start: 0.7018 (m-30) cc_final: 0.6768 (m-30) REVERT: Y 157 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7960 (mtpt) REVERT: Y 232 ARG cc_start: 0.7999 (mmm-85) cc_final: 0.7592 (mmm-85) REVERT: Y 276 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7770 (ttpp) REVERT: Y 297 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: Y 300 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7223 (mtm) REVERT: Z 311 ARG cc_start: 0.8374 (mpp80) cc_final: 0.8121 (mtt180) outliers start: 148 outliers final: 97 residues processed: 920 average time/residue: 0.6382 time to fit residues: 675.2082 Evaluate side-chains 978 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 862 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1143 VAL Chi-restraints excluded: chain Q residue 1169 THR Chi-restraints excluded: chain Q residue 1184 GLU Chi-restraints excluded: chain Q residue 1203 LEU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1321 TYR Chi-restraints excluded: chain Q residue 1371 LEU Chi-restraints excluded: chain Q residue 1415 ARG Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 677 VAL Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 241 LYS Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 282 GLU Chi-restraints excluded: chain T residue 283 LYS Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain T residue 300 VAL Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 363 LEU Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 397 SER Chi-restraints excluded: chain T residue 402 LEU Chi-restraints excluded: chain T residue 429 SER Chi-restraints excluded: chain T residue 433 GLU Chi-restraints excluded: chain T residue 441 GLU Chi-restraints excluded: chain T residue 456 LEU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 226 GLU Chi-restraints excluded: chain U residue 283 GLU Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 146 GLU Chi-restraints excluded: chain V residue 190 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 294 LYS Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain V residue 443 LYS Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 208 ARG Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 234 THR Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 421 GLU Chi-restraints excluded: chain W residue 423 VAL Chi-restraints excluded: chain X residue 31 LYS Chi-restraints excluded: chain X residue 35 LEU Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 198 ASP Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 203 GLU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 214 ARG Chi-restraints excluded: chain X residue 245 GLN Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 454 LYS Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 185 LEU Chi-restraints excluded: chain Y residue 193 ASP Chi-restraints excluded: chain Y residue 229 LEU Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 276 LYS Chi-restraints excluded: chain Y residue 297 GLU Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 304 GLU Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 331 LYS Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 432 ASP Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 83 optimal weight: 1.9990 chunk 234 optimal weight: 0.3980 chunk 236 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 318 optimal weight: 0.9990 chunk 357 optimal weight: 0.0970 chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 238 optimal weight: 0.7980 chunk 4 optimal weight: 0.1980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 611 GLN U 63 ASN U 230 GLN U 274 ASN U 310 ASN V 205 ASN X 256 ASN X 289 ASN X 325 ASN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.130899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110866 restraints weight = 39691.032| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.84 r_work: 0.3355 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29100 Z= 0.117 Angle : 0.548 9.745 39368 Z= 0.271 Chirality : 0.043 0.159 4620 Planarity : 0.004 0.080 5039 Dihedral : 8.177 175.960 4006 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.21 % Allowed : 25.47 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.14), residues: 3618 helix: 0.94 (0.14), residues: 1538 sheet: 0.81 (0.20), residues: 638 loop : -0.97 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.000 ARG Q1142 TYR 0.023 0.001 TYR X 323 PHE 0.022 0.001 PHE R 691 TRP 0.016 0.001 TRP Y 280 HIS 0.012 0.001 HIS V 27 Details of bonding type rmsd covalent geometry : bond 0.00276 (29098) covalent geometry : angle 0.54754 (39368) hydrogen bonds : bond 0.03644 ( 1092) hydrogen bonds : angle 3.87375 ( 3174) Misc. bond : bond 0.00514 ( 2) *********************** 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 1009 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 876 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.7901 (p0) cc_final: 0.7195 (p0) REVERT: Q 1139 GLU cc_start: 0.7527 (tp30) cc_final: 0.7214 (tp30) REVERT: Q 1143 VAL cc_start: 0.7631 (OUTLIER) cc_final: 0.7062 (p) REVERT: Q 1167 PHE cc_start: 0.7527 (m-80) cc_final: 0.7145 (m-10) REVERT: Q 1184 GLU cc_start: 0.5983 (OUTLIER) cc_final: 0.5678 (pp20) REVERT: Q 1302 ARG cc_start: 0.7271 (ttt180) cc_final: 0.7004 (ttt180) REVERT: Q 1321 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6554 (t80) REVERT: Q 1327 MET cc_start: 0.5122 (mmm) cc_final: 0.4728 (tmm) REVERT: Q 1405 MET cc_start: 0.7962 (mpp) cc_final: 0.7538 (mpp) REVERT: R 263 LYS cc_start: 0.8757 (ptmm) cc_final: 0.8554 (ptmm) REVERT: R 659 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7327 (mm-40) REVERT: R 687 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7751 (mm-30) REVERT: R 719 ARG cc_start: 0.7704 (mpp80) cc_final: 0.7145 (mpp-170) REVERT: R 736 GLU cc_start: 0.7545 (tt0) cc_final: 0.7295 (tt0) REVERT: T 241 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8355 (ttmt) REVERT: T 431 ARG cc_start: 0.8356 (mtm-85) cc_final: 0.7984 (mtm180) REVERT: T 456 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8404 (mp) REVERT: U 228 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7431 (mm-30) REVERT: U 230 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7566 (tp40) REVERT: U 254 PHE cc_start: 0.8336 (p90) cc_final: 0.8122 (p90) REVERT: U 350 ARG cc_start: 0.8411 (mtt90) cc_final: 0.8160 (mtt-85) REVERT: V 268 MET cc_start: 0.8170 (mmm) cc_final: 0.7860 (mmm) REVERT: V 319 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7641 (mm-30) REVERT: V 412 LEU cc_start: 0.8283 (tp) cc_final: 0.8068 (tp) REVERT: V 428 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8370 (t) REVERT: W 208 ARG cc_start: 0.5818 (OUTLIER) cc_final: 0.4808 (tpt-90) REVERT: W 220 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7147 (mpp80) REVERT: W 438 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7685 (tppp) REVERT: X 35 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8564 (mt) REVERT: X 37 GLU cc_start: 0.7250 (pm20) cc_final: 0.6889 (pm20) REVERT: X 94 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7453 (mt0) REVERT: X 203 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6753 (pm20) REVERT: Y 23 HIS cc_start: 0.8474 (OUTLIER) cc_final: 0.6765 (p90) REVERT: Y 134 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7464 (mp0) REVERT: Y 139 GLU cc_start: 0.7919 (tt0) cc_final: 0.7705 (tt0) REVERT: Y 157 LYS cc_start: 0.8362 (tppp) cc_final: 0.8059 (mptp) REVERT: Y 276 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7663 (ttpp) REVERT: Y 297 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: Y 300 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7004 (mtm) outliers start: 133 outliers final: 85 residues processed: 933 average time/residue: 0.6406 time to fit residues: 686.2515 Evaluate side-chains 970 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 868 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1143 VAL Chi-restraints excluded: chain Q residue 1184 GLU Chi-restraints excluded: chain Q residue 1203 LEU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1321 TYR Chi-restraints excluded: chain Q residue 1415 ARG Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 278 GLU Chi-restraints excluded: chain R residue 677 VAL Chi-restraints excluded: chain R residue 703 SER Chi-restraints excluded: chain R residue 723 GLN Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 150 GLU Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 241 LYS Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain T residue 300 VAL Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 363 LEU Chi-restraints excluded: chain T residue 402 LEU Chi-restraints excluded: chain T residue 433 GLU Chi-restraints excluded: chain T residue 441 GLU Chi-restraints excluded: chain T residue 456 LEU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 226 GLU Chi-restraints excluded: chain U residue 230 GLN Chi-restraints excluded: chain U residue 281 LYS Chi-restraints excluded: chain U residue 283 GLU Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 190 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 385 GLU Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 208 ARG Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 234 THR Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 421 GLU Chi-restraints excluded: chain W residue 423 VAL Chi-restraints excluded: chain X residue 35 LEU Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 198 ASP Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 203 GLU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 245 GLN Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 185 LEU Chi-restraints excluded: chain Y residue 193 ASP Chi-restraints excluded: chain Y residue 229 LEU Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 276 LYS Chi-restraints excluded: chain Y residue 297 GLU Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 304 GLU Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 331 LYS Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 432 ASP Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 329 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 201 optimal weight: 1.9990 chunk 330 optimal weight: 0.7980 chunk 308 optimal weight: 0.9980 chunk 158 optimal weight: 0.0970 chunk 18 optimal weight: 0.5980 chunk 200 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 288 optimal weight: 0.1980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 592 HIS R 611 GLN R 745 HIS T 256 ASN U 63 ASN U 274 ASN U 310 ASN V 205 ASN V 394 GLN X 124 ASN X 256 ASN X 289 ASN X 325 ASN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.131168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.110996 restraints weight = 39685.663| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.85 r_work: 0.3360 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29100 Z= 0.113 Angle : 0.553 11.677 39368 Z= 0.272 Chirality : 0.043 0.161 4620 Planarity : 0.004 0.077 5039 Dihedral : 8.078 175.862 4006 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.80 % Allowed : 26.49 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.14), residues: 3618 helix: 1.00 (0.14), residues: 1540 sheet: 0.84 (0.20), residues: 651 loop : -0.96 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q1142 TYR 0.028 0.001 TYR R 34 PHE 0.022 0.001 PHE R 691 TRP 0.013 0.001 TRP Y 280 HIS 0.010 0.001 HIS V 27 Details of bonding type rmsd covalent geometry : bond 0.00265 (29098) covalent geometry : angle 0.55319 (39368) hydrogen bonds : bond 0.03530 ( 1092) hydrogen bonds : angle 3.85493 ( 3174) Misc. bond : bond 0.00466 ( 2) *********************** 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 989 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 869 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.7885 (p0) cc_final: 0.7182 (p0) REVERT: Q 1139 GLU cc_start: 0.7561 (tp30) cc_final: 0.7240 (tp30) REVERT: Q 1143 VAL cc_start: 0.7622 (OUTLIER) cc_final: 0.7073 (p) REVERT: Q 1167 PHE cc_start: 0.7517 (m-80) cc_final: 0.7061 (m-80) REVERT: Q 1168 LYS cc_start: 0.7889 (tppt) cc_final: 0.7573 (mppt) REVERT: Q 1184 GLU cc_start: 0.5955 (OUTLIER) cc_final: 0.5655 (pp20) REVERT: Q 1302 ARG cc_start: 0.7274 (ttt180) cc_final: 0.7004 (ttt180) REVERT: Q 1321 TYR cc_start: 0.7355 (OUTLIER) cc_final: 0.6570 (t80) REVERT: Q 1327 MET cc_start: 0.5084 (mmm) cc_final: 0.4674 (tmm) REVERT: Q 1405 MET cc_start: 0.7939 (mpp) cc_final: 0.7505 (mpp) REVERT: R 90 GLN cc_start: 0.7442 (tp-100) cc_final: 0.7130 (tp-100) REVERT: R 659 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7385 (mm-40) REVERT: R 687 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7729 (mm-30) REVERT: R 719 ARG cc_start: 0.7706 (mpp80) cc_final: 0.7154 (mpp-170) REVERT: R 736 GLU cc_start: 0.7542 (tt0) cc_final: 0.7295 (tt0) REVERT: T 241 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8351 (ttmt) REVERT: T 431 ARG cc_start: 0.8315 (mtm-85) cc_final: 0.7928 (mtm110) REVERT: U 350 ARG cc_start: 0.8386 (mtt90) cc_final: 0.8146 (mtt-85) REVERT: V 268 MET cc_start: 0.8188 (mmm) cc_final: 0.7948 (mmm) REVERT: V 386 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.8248 (mmm160) REVERT: V 412 LEU cc_start: 0.8252 (tp) cc_final: 0.8038 (tp) REVERT: V 428 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8362 (t) REVERT: V 433 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6732 (tm-30) REVERT: W 208 ARG cc_start: 0.5805 (OUTLIER) cc_final: 0.4722 (tpt-90) REVERT: W 438 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7566 (tppp) REVERT: X 35 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8548 (mt) REVERT: X 37 GLU cc_start: 0.7252 (pm20) cc_final: 0.6896 (pm20) REVERT: X 94 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7434 (mt0) REVERT: X 203 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6757 (pm20) REVERT: Y 23 HIS cc_start: 0.8484 (OUTLIER) cc_final: 0.6703 (p90) REVERT: Y 139 GLU cc_start: 0.7886 (tt0) cc_final: 0.7673 (tt0) REVERT: Y 157 LYS cc_start: 0.8416 (tppp) cc_final: 0.7970 (mtpt) REVERT: Y 232 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7530 (mmm-85) REVERT: Y 276 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7646 (ttpp) REVERT: Y 300 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.6971 (mtm) outliers start: 120 outliers final: 82 residues processed: 920 average time/residue: 0.6415 time to fit residues: 681.2524 Evaluate side-chains 948 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 854 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1143 VAL Chi-restraints excluded: chain Q residue 1184 GLU Chi-restraints excluded: chain Q residue 1203 LEU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1321 TYR Chi-restraints excluded: chain Q residue 1371 LEU Chi-restraints excluded: chain Q residue 1415 ARG Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 278 GLU Chi-restraints excluded: chain R residue 703 SER Chi-restraints excluded: chain R residue 723 GLN Chi-restraints excluded: chain R residue 728 VAL Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 150 GLU Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 241 LYS Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain T residue 300 VAL Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 402 LEU Chi-restraints excluded: chain T residue 441 GLU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 281 LYS Chi-restraints excluded: chain U residue 283 GLU Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 421 GLU Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 190 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain V residue 443 LYS Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 208 ARG Chi-restraints excluded: chain W residue 234 THR Chi-restraints excluded: chain W residue 285 LYS Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 421 GLU Chi-restraints excluded: chain W residue 423 VAL Chi-restraints excluded: chain X residue 35 LEU Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 198 ASP Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 203 GLU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 245 GLN Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 193 ASP Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 276 LYS Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 304 GLU Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 331 LYS Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 432 ASP Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 274 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 257 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 14 optimal weight: 0.0980 chunk 264 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 16 optimal weight: 0.0040 chunk 103 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 611 GLN R 745 HIS U 63 ASN U 274 ASN U 310 ASN V 205 ASN V 394 GLN X 256 ASN X 289 ASN X 325 ASN Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.130929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110740 restraints weight = 39652.053| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.87 r_work: 0.3356 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29100 Z= 0.120 Angle : 0.563 11.472 39368 Z= 0.277 Chirality : 0.043 0.185 4620 Planarity : 0.004 0.068 5039 Dihedral : 8.007 176.247 4006 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.73 % Allowed : 26.55 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.14), residues: 3618 helix: 0.98 (0.14), residues: 1547 sheet: 0.84 (0.20), residues: 646 loop : -0.92 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q1142 TYR 0.030 0.001 TYR R 34 PHE 0.022 0.001 PHE R 691 TRP 0.016 0.001 TRP Y 280 HIS 0.008 0.001 HIS V 27 Details of bonding type rmsd covalent geometry : bond 0.00283 (29098) covalent geometry : angle 0.56298 (39368) hydrogen bonds : bond 0.03645 ( 1092) hydrogen bonds : angle 3.86410 ( 3174) Misc. bond : bond 0.00460 ( 2) *********************** 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 993 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 875 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.7884 (p0) cc_final: 0.7230 (p0) REVERT: Q 1139 GLU cc_start: 0.7565 (tp30) cc_final: 0.7227 (tp30) REVERT: Q 1143 VAL cc_start: 0.7579 (OUTLIER) cc_final: 0.7043 (p) REVERT: Q 1167 PHE cc_start: 0.7520 (m-80) cc_final: 0.7178 (m-80) REVERT: Q 1184 GLU cc_start: 0.5966 (OUTLIER) cc_final: 0.5673 (pp20) REVERT: Q 1302 ARG cc_start: 0.7310 (ttt180) cc_final: 0.7037 (ttt180) REVERT: Q 1321 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.6567 (t80) REVERT: Q 1327 MET cc_start: 0.5093 (mmm) cc_final: 0.4653 (tmm) REVERT: Q 1405 MET cc_start: 0.7982 (mpp) cc_final: 0.7529 (mpp) REVERT: R 74 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.8053 (tmmt) REVERT: R 90 GLN cc_start: 0.7427 (tp-100) cc_final: 0.7106 (tp-100) REVERT: R 659 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7452 (mm-40) REVERT: R 676 LYS cc_start: 0.6075 (ptpt) cc_final: 0.4130 (ptpp) REVERT: R 687 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7714 (mm-30) REVERT: R 719 ARG cc_start: 0.7694 (mpp80) cc_final: 0.7136 (mpp-170) REVERT: R 736 GLU cc_start: 0.7556 (tt0) cc_final: 0.7290 (tt0) REVERT: T 190 GLN cc_start: 0.7954 (mt0) cc_final: 0.7716 (mt0) REVERT: T 241 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8358 (ttmt) REVERT: T 431 ARG cc_start: 0.8303 (mtm-85) cc_final: 0.7946 (mtm180) REVERT: U 350 ARG cc_start: 0.8391 (mtt90) cc_final: 0.8131 (mtt-85) REVERT: U 450 ASP cc_start: 0.7837 (m-30) cc_final: 0.7601 (m-30) REVERT: V 268 MET cc_start: 0.8180 (mmm) cc_final: 0.7925 (mmm) REVERT: V 412 LEU cc_start: 0.8255 (tp) cc_final: 0.8053 (tp) REVERT: V 428 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8360 (t) REVERT: W 208 ARG cc_start: 0.5774 (OUTLIER) cc_final: 0.4722 (tpt-90) REVERT: X 35 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8551 (mt) REVERT: X 37 GLU cc_start: 0.7264 (pm20) cc_final: 0.6908 (pm20) REVERT: X 70 MET cc_start: 0.7829 (mpp) cc_final: 0.6832 (mpp) REVERT: X 94 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7425 (mt0) REVERT: X 203 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6778 (pm20) REVERT: Y 23 HIS cc_start: 0.8495 (OUTLIER) cc_final: 0.6692 (p90) REVERT: Y 134 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7448 (mp0) REVERT: Y 139 GLU cc_start: 0.7878 (tt0) cc_final: 0.7654 (tt0) REVERT: Y 157 LYS cc_start: 0.8393 (tppp) cc_final: 0.8117 (mptp) REVERT: Y 276 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7599 (ttpp) REVERT: Y 300 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7012 (mtm) outliers start: 118 outliers final: 81 residues processed: 922 average time/residue: 0.6664 time to fit residues: 705.2032 Evaluate side-chains 963 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 869 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL Chi-restraints excluded: chain Q residue 1071 THR Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1143 VAL Chi-restraints excluded: chain Q residue 1184 GLU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1321 TYR Chi-restraints excluded: chain Q residue 1371 LEU Chi-restraints excluded: chain Q residue 1415 ARG Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 150 GLU Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 241 LYS Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain T residue 300 VAL Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 402 LEU Chi-restraints excluded: chain T residue 429 SER Chi-restraints excluded: chain T residue 441 GLU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 226 GLU Chi-restraints excluded: chain U residue 281 LYS Chi-restraints excluded: chain U residue 283 GLU Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 190 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 208 ARG Chi-restraints excluded: chain W residue 234 THR Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 421 GLU Chi-restraints excluded: chain W residue 423 VAL Chi-restraints excluded: chain X residue 31 LYS Chi-restraints excluded: chain X residue 35 LEU Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 198 ASP Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 203 GLU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 214 ARG Chi-restraints excluded: chain X residue 245 GLN Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 444 LEU Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 185 LEU Chi-restraints excluded: chain Y residue 193 ASP Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 276 LYS Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 304 GLU Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 331 LYS Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 432 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 278 optimal weight: 0.3980 chunk 129 optimal weight: 0.4980 chunk 325 optimal weight: 1.9990 chunk 217 optimal weight: 0.3980 chunk 286 optimal weight: 0.7980 chunk 165 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 198 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 ASN R 611 GLN R 745 HIS T 256 ASN T 298 GLN ** T 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN U 274 ASN U 310 ASN V 205 ASN V 394 GLN ** X 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 256 ASN X 289 ASN X 325 ASN Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.130889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110747 restraints weight = 39519.559| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.85 r_work: 0.3355 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29100 Z= 0.129 Angle : 0.578 10.994 39368 Z= 0.285 Chirality : 0.044 0.189 4620 Planarity : 0.004 0.069 5039 Dihedral : 7.997 176.061 4006 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.13 % Allowed : 27.12 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.14), residues: 3618 helix: 0.97 (0.14), residues: 1545 sheet: 0.84 (0.20), residues: 643 loop : -0.92 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q1142 TYR 0.030 0.001 TYR R 34 PHE 0.022 0.001 PHE R 691 TRP 0.013 0.001 TRP Y 280 HIS 0.008 0.001 HIS V 27 Details of bonding type rmsd covalent geometry : bond 0.00308 (29098) covalent geometry : angle 0.57840 (39368) hydrogen bonds : bond 0.03763 ( 1092) hydrogen bonds : angle 3.90374 ( 3174) Misc. bond : bond 0.00457 ( 2) ********************** 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 956 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 857 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.7933 (p0) cc_final: 0.7102 (p0) REVERT: Q 1139 GLU cc_start: 0.7546 (tp30) cc_final: 0.7219 (tp30) REVERT: Q 1143 VAL cc_start: 0.7616 (OUTLIER) cc_final: 0.7079 (p) REVERT: Q 1167 PHE cc_start: 0.7512 (m-80) cc_final: 0.6989 (m-80) REVERT: Q 1168 LYS cc_start: 0.7897 (tppt) cc_final: 0.7585 (mppt) REVERT: Q 1184 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5607 (pp20) REVERT: Q 1302 ARG cc_start: 0.7289 (ttt180) cc_final: 0.7022 (ttt180) REVERT: Q 1321 TYR cc_start: 0.7309 (OUTLIER) cc_final: 0.6542 (t80) REVERT: Q 1327 MET cc_start: 0.5066 (mmm) cc_final: 0.4632 (tmm) REVERT: Q 1405 MET cc_start: 0.7989 (mpp) cc_final: 0.7523 (mpp) REVERT: R 74 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8068 (tmmt) REVERT: R 84 ASN cc_start: 0.8482 (m110) cc_final: 0.8271 (m-40) REVERT: R 90 GLN cc_start: 0.7425 (tp-100) cc_final: 0.7109 (tp-100) REVERT: R 659 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7490 (mm-40) REVERT: R 676 LYS cc_start: 0.6055 (ptpt) cc_final: 0.4142 (ptpp) REVERT: R 682 GLU cc_start: 0.8165 (mp0) cc_final: 0.7865 (mp0) REVERT: R 687 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7739 (mm-30) REVERT: R 719 ARG cc_start: 0.7705 (mpp80) cc_final: 0.7149 (mpp-170) REVERT: R 736 GLU cc_start: 0.7526 (tt0) cc_final: 0.7269 (tt0) REVERT: T 241 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8366 (ttmt) REVERT: T 431 ARG cc_start: 0.8306 (mtm-85) cc_final: 0.7952 (mtm110) REVERT: U 350 ARG cc_start: 0.8329 (mtt90) cc_final: 0.8094 (mtt-85) REVERT: U 450 ASP cc_start: 0.7807 (m-30) cc_final: 0.7560 (m-30) REVERT: V 268 MET cc_start: 0.8180 (mmm) cc_final: 0.7918 (mmm) REVERT: V 394 GLN cc_start: 0.8413 (mt0) cc_final: 0.8090 (mt0) REVERT: V 428 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8352 (t) REVERT: W 208 ARG cc_start: 0.5773 (OUTLIER) cc_final: 0.4716 (tpt-90) REVERT: X 35 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8551 (mt) REVERT: X 37 GLU cc_start: 0.7254 (pm20) cc_final: 0.6918 (pm20) REVERT: X 94 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7444 (mt0) REVERT: X 203 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6797 (pm20) REVERT: Y 23 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.6706 (p90) REVERT: Y 134 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7458 (mp0) REVERT: Y 157 LYS cc_start: 0.8423 (tppp) cc_final: 0.8148 (mptp) REVERT: Y 276 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7512 (ttpp) REVERT: Y 300 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7075 (mtm) REVERT: Y 374 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7216 (tm-30) outliers start: 99 outliers final: 73 residues processed: 899 average time/residue: 0.6414 time to fit residues: 662.7357 Evaluate side-chains 942 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 856 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL Chi-restraints excluded: chain Q residue 1101 ASP Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1143 VAL Chi-restraints excluded: chain Q residue 1184 GLU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1321 TYR Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 723 GLN Chi-restraints excluded: chain S residue 49 LYS Chi-restraints excluded: chain S residue 104 GLU Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 150 GLU Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 241 LYS Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 300 VAL Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 402 LEU Chi-restraints excluded: chain T residue 441 GLU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 60 MET Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 226 GLU Chi-restraints excluded: chain U residue 281 LYS Chi-restraints excluded: chain U residue 283 GLU Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 190 GLN Chi-restraints excluded: chain V residue 193 LYS Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 198 LYS Chi-restraints excluded: chain W residue 208 ARG Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 421 GLU Chi-restraints excluded: chain W residue 423 VAL Chi-restraints excluded: chain X residue 31 LYS Chi-restraints excluded: chain X residue 35 LEU Chi-restraints excluded: chain X residue 42 LYS Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 198 ASP Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 203 GLU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 214 ARG Chi-restraints excluded: chain X residue 245 GLN Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 33 GLU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 185 LEU Chi-restraints excluded: chain Y residue 193 ASP Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 276 LYS Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 304 GLU Chi-restraints excluded: chain Y residue 330 SER Chi-restraints excluded: chain Y residue 331 LYS Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 432 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 77 optimal weight: 0.6980 chunk 234 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 311 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 232 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 ASN R 611 GLN ** R 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 745 HIS T 325 ASN ** T 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN U 119 GLN U 242 HIS U 274 ASN U 310 ASN V 205 ASN X 124 ASN X 256 ASN X 289 ASN X 325 ASN Y 23 HIS Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 441 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.129178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.109018 restraints weight = 39671.602| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.84 r_work: 0.3330 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29100 Z= 0.181 Angle : 0.624 11.248 39368 Z= 0.309 Chirality : 0.046 0.214 4620 Planarity : 0.004 0.078 5039 Dihedral : 8.186 177.277 4004 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.10 % Allowed : 27.03 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.14), residues: 3618 helix: 0.85 (0.14), residues: 1543 sheet: 0.80 (0.20), residues: 644 loop : -0.98 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q1142 TYR 0.031 0.002 TYR R 34 PHE 0.020 0.002 PHE R 691 TRP 0.012 0.001 TRP Y 280 HIS 0.008 0.001 HIS V 27 Details of bonding type rmsd covalent geometry : bond 0.00440 (29098) covalent geometry : angle 0.62400 (39368) hydrogen bonds : bond 0.04598 ( 1092) hydrogen bonds : angle 4.02685 ( 3174) Misc. bond : bond 0.00580 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13923.79 seconds wall clock time: 236 minutes 33.03 seconds (14193.03 seconds total)