Starting phenix.real_space_refine on Mon May 26 18:44:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8etw_28601/05_2025/8etw_28601_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8etw_28601/05_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_28601/05_2025/8etw_28601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8etw_28601/05_2025/8etw_28601.map" model { file = "/net/cci-nas-00/data/ceres_data/8etw_28601/05_2025/8etw_28601_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8etw_28601/05_2025/8etw_28601_neut.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 17.32, per 1000 atoms: 0.60 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: 6.36 Conformation dependent library (CDL) restraints added in 3.6 seconds 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6820 Finding SS restraints... Secondary structure from input PDB file: 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: 3.50 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: 10.45 Time building geometry restraints manager: 7.48 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 463 or resid 501)) selection = (chain 'V' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 463 or resid 501)) selection = (chain 'X' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 463 or resid 501)) } ncs_group { reference = (chain 'U' and (resid 18 through 459 or resid 501)) selection = (chain 'W' and (resid 18 through 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)) 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: 7.520 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: 1.220 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 62.040 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.150 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:13.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.270 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (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 TRP 0.018 0.002 TRP Y 280 HIS 0.008 0.001 HIS T 250 PHE 0.046 0.002 PHE Q1167 TYR 0.050 0.002 TYR X 323 ARG 0.019 0.001 ARG S 73 Details of bonding type rmsd hydrogen bonds : bond 0.17591 ( 1092) hydrogen bonds : angle 6.24394 ( 3174) covalent geometry : bond 0.00528 (29098) covalent geometry : angle 0.90986 (39368) 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 : 3.292 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: 1.6181 time to fit residues: 1589.4489 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 : 3.230 ------------------------------------------------------------------------------- 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 304 optimal weight: 0.0270 chunk 273 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 146 optimal weight: 0.5980 chunk 282 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 172 optimal weight: 0.5980 chunk 210 optimal weight: 0.1980 chunk 327 optimal weight: 2.9990 overall best weight: 0.4840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1117 ASN Q1204 ASN 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.131338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111114 restraints weight = 39708.510| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.00 r_work: 0.3353 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 29100 Z= 0.136 Angle : 0.586 11.011 39368 Z= 0.294 Chirality : 0.043 0.204 4620 Planarity : 0.005 0.097 5039 Dihedral : 8.545 147.909 4010 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.73 % Allowed : 24.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 3618 helix: -0.07 (0.13), residues: 1522 sheet: 0.64 (0.20), residues: 646 loop : -1.20 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 280 HIS 0.003 0.001 HIS Y 237 PHE 0.024 0.001 PHE R 691 TYR 0.018 0.001 TYR V 201 ARG 0.012 0.000 ARG Q1142 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 1092) hydrogen bonds : angle 4.29667 ( 3174) covalent geometry : bond 0.00318 (29098) covalent geometry : angle 0.58623 (39368) Misc. bond : bond 0.00288 ( 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 1015 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 897 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1000 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6358 (tp) REVERT: Q 1016 LEU cc_start: 0.8289 (mm) cc_final: 0.8082 (mm) REVERT: Q 1103 ASP cc_start: 0.7642 (p0) cc_final: 0.7153 (p0) REVERT: Q 1139 GLU cc_start: 0.7493 (tp30) cc_final: 0.7210 (tp30) REVERT: Q 1167 PHE cc_start: 0.7351 (m-10) cc_final: 0.6970 (m-80) REVERT: Q 1405 MET cc_start: 0.7900 (mpp) cc_final: 0.7488 (mpp) REVERT: R 101 ASP cc_start: 0.7475 (t0) cc_final: 0.7209 (t0) REVERT: R 146 GLN cc_start: 0.8011 (tp40) cc_final: 0.7793 (mm-40) REVERT: R 243 TYR cc_start: 0.7670 (m-10) cc_final: 0.7349 (m-10) REVERT: R 256 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7861 (OUTLIER) REVERT: R 687 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7724 (mm-30) REVERT: S 80 LYS cc_start: 0.8543 (tppt) cc_final: 0.8314 (tppt) REVERT: S 154 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7291 (mm-30) REVERT: T 241 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8301 (ttmt) REVERT: T 364 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8126 (tp) REVERT: T 431 ARG cc_start: 0.8332 (mtm-85) cc_final: 0.8048 (mtm110) REVERT: U 350 ARG cc_start: 0.8546 (mtt90) cc_final: 0.8258 (mtt-85) REVERT: V 165 HIS cc_start: 0.8078 (m90) cc_final: 0.7823 (m90) REVERT: V 268 MET cc_start: 0.8146 (tpp) cc_final: 0.7847 (tpp) REVERT: V 325 ASN cc_start: 0.8181 (m-40) cc_final: 0.7970 (m-40) REVERT: V 451 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8169 (mtp180) REVERT: W 330 SER cc_start: 0.8195 (p) cc_final: 0.7988 (m) REVERT: X 37 GLU cc_start: 0.7374 (pm20) cc_final: 0.6951 (pm20) REVERT: X 94 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7532 (mt0) REVERT: X 171 LYS cc_start: 0.8803 (tttt) cc_final: 0.8599 (tttp) REVERT: X 242 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6774 (mm-30) REVERT: Y 132 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7177 (mp0) REVERT: Y 276 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7400 (ttpp) REVERT: Z 311 ARG cc_start: 0.8337 (mpp80) cc_final: 0.8089 (mtt-85) outliers start: 118 outliers final: 52 residues processed: 949 average time/residue: 1.5654 time to fit residues: 1699.5311 Evaluate side-chains 914 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 856 time to evaluate : 3.215 ------------------------------------------------------------------------------- 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 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 256 ASN 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 49 VAL 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 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 U residue 438 LYS Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 146 GLU 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 206 THR 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 157 LYS Chi-restraints excluded: chain Y residue 168 ILE 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 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 175 optimal weight: 2.9990 chunk 256 optimal weight: 0.0570 chunk 340 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 330 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 348 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 119 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 56 HIS R 611 GLN T 29 HIS T 256 ASN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 441 GLN V 205 ASN V 394 GLN W 326 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.130278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.110110 restraints weight = 39779.003| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.85 r_work: 0.3344 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29100 Z= 0.150 Angle : 0.576 11.206 39368 Z= 0.286 Chirality : 0.044 0.143 4620 Planarity : 0.004 0.140 5039 Dihedral : 8.225 137.614 4006 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.40 % Allowed : 23.39 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3618 helix: 0.48 (0.13), residues: 1528 sheet: 0.66 (0.20), residues: 641 loop : -1.11 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 280 HIS 0.004 0.001 HIS R 56 PHE 0.022 0.001 PHE R 691 TYR 0.023 0.001 TYR X 323 ARG 0.018 0.000 ARG Q1142 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 1092) hydrogen bonds : angle 4.06976 ( 3174) covalent geometry : bond 0.00359 (29098) covalent geometry : angle 0.57621 (39368) Misc. bond : bond 0.00760 ( 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 1020 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 881 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1016 LEU cc_start: 0.8324 (mm) cc_final: 0.8071 (mm) REVERT: Q 1103 ASP cc_start: 0.7831 (p0) cc_final: 0.7181 (p0) REVERT: Q 1139 GLU cc_start: 0.7478 (tp30) cc_final: 0.7145 (tp30) REVERT: Q 1143 VAL cc_start: 0.8025 (OUTLIER) cc_final: 0.7372 (p) REVERT: Q 1167 PHE cc_start: 0.7480 (m-10) cc_final: 0.7132 (m-80) REVERT: Q 1184 GLU cc_start: 0.5959 (OUTLIER) cc_final: 0.5662 (pp20) REVERT: Q 1321 TYR cc_start: 0.7267 (m-80) cc_final: 0.6541 (t80) REVERT: Q 1405 MET cc_start: 0.7903 (mpp) cc_final: 0.7540 (mpp) REVERT: R 101 ASP cc_start: 0.7545 (t0) cc_final: 0.7244 (t0) REVERT: R 146 GLN cc_start: 0.8037 (tp40) cc_final: 0.7834 (mm-40) REVERT: R 687 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7718 (mm-30) REVERT: R 736 GLU cc_start: 0.7681 (tt0) cc_final: 0.7443 (tt0) REVERT: T 241 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8331 (ttmt) REVERT: T 364 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8145 (tp) REVERT: T 431 ARG cc_start: 0.8352 (mtm-85) cc_final: 0.8060 (mtm180) REVERT: U 350 ARG cc_start: 0.8542 (mtt90) cc_final: 0.8269 (mtt-85) REVERT: U 413 ARG cc_start: 0.8451 (mtp-110) cc_final: 0.8160 (mtp-110) REVERT: V 319 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7697 (mm-30) REVERT: V 341 ASN cc_start: 0.8662 (p0) cc_final: 0.8214 (p0) REVERT: V 451 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8116 (mtp180) REVERT: W 38 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8212 (mtt180) REVERT: W 208 ARG cc_start: 0.5812 (OUTLIER) cc_final: 0.4790 (tpt-90) REVERT: W 326 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8387 (p0) REVERT: W 438 LYS cc_start: 0.8120 (ttmm) cc_final: 0.7638 (tppp) REVERT: X 37 GLU cc_start: 0.7324 (pm20) cc_final: 0.6937 (pm20) REVERT: X 56 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7723 (mt-10) REVERT: X 94 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7525 (mt0) REVERT: X 203 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6779 (pm20) REVERT: Y 132 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7182 (mp0) REVERT: Y 134 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7471 (mp0) REVERT: Y 276 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7536 (ttpp) REVERT: Y 300 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.6897 (mtm) REVERT: Z 311 ARG cc_start: 0.8359 (mpp80) cc_final: 0.8114 (mtt-85) outliers start: 139 outliers final: 74 residues processed: 936 average time/residue: 1.5612 time to fit residues: 1674.7670 Evaluate side-chains 935 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 849 time to evaluate : 3.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 432 LYS 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 330 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 V residue 133 ILE Chi-restraints excluded: chain V residue 171 LYS 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 411 SER 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 326 ASN 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 203 GLU 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 X residue 454 LYS 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 103 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 304 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 251 optimal weight: 0.5980 chunk 186 optimal weight: 1.9990 chunk 327 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 177 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 55 ASN R 144 GLN R 611 GLN T 256 ASN U 63 ASN U 274 ASN U 310 ASN U 441 GLN V 205 ASN V 325 ASN W 326 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.129700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109506 restraints weight = 40082.473| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.86 r_work: 0.3331 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1443 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= 0.170 Angle : 0.585 9.541 39368 Z= 0.291 Chirality : 0.044 0.151 4620 Planarity : 0.004 0.104 5039 Dihedral : 8.617 178.948 4006 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.68 % Allowed : 24.05 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3618 helix: 0.66 (0.14), residues: 1529 sheet: 0.68 (0.20), residues: 645 loop : -1.10 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 280 HIS 0.006 0.001 HIS V 165 PHE 0.020 0.001 PHE R 691 TYR 0.020 0.002 TYR V 201 ARG 0.015 0.000 ARG Q1142 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 1092) hydrogen bonds : angle 4.05434 ( 3174) covalent geometry : bond 0.00410 (29098) covalent geometry : angle 0.58464 (39368) Misc. bond : bond 0.00632 ( 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 1016 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 868 time to evaluate : 3.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1016 LEU cc_start: 0.8340 (mm) cc_final: 0.8085 (mm) REVERT: Q 1103 ASP cc_start: 0.7964 (p0) cc_final: 0.7261 (p0) REVERT: Q 1139 GLU cc_start: 0.7474 (tp30) cc_final: 0.7205 (tp30) REVERT: Q 1143 VAL cc_start: 0.8023 (OUTLIER) cc_final: 0.7412 (p) REVERT: Q 1167 PHE cc_start: 0.7569 (m-10) cc_final: 0.7233 (m-80) REVERT: Q 1184 GLU cc_start: 0.5998 (OUTLIER) cc_final: 0.5693 (pp20) REVERT: Q 1302 ARG cc_start: 0.7296 (ttt180) cc_final: 0.7023 (ttt180) REVERT: Q 1321 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.6563 (t80) REVERT: Q 1405 MET cc_start: 0.7917 (mpp) cc_final: 0.7599 (mtm) REVERT: R 74 LYS cc_start: 0.8354 (ttpp) cc_final: 0.8132 (tmmt) REVERT: R 146 GLN cc_start: 0.8022 (tp40) cc_final: 0.7818 (mm-40) REVERT: R 242 GLN cc_start: 0.8153 (mt0) cc_final: 0.7613 (mt0) REVERT: R 687 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7704 (mm-30) REVERT: R 736 GLU cc_start: 0.7667 (tt0) cc_final: 0.7415 (tt0) REVERT: T 241 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8343 (ttmt) REVERT: T 364 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8156 (tp) REVERT: U 66 ILE cc_start: 0.8482 (pp) cc_final: 0.8258 (mp) REVERT: U 254 PHE cc_start: 0.8333 (p90) cc_final: 0.8101 (p90) REVERT: U 350 ARG cc_start: 0.8527 (mtt90) cc_final: 0.8256 (mtt-85) REVERT: U 413 ARG cc_start: 0.8460 (mtp-110) cc_final: 0.8258 (mtp-110) REVERT: W 38 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8241 (mtt180) REVERT: W 208 ARG cc_start: 0.5832 (OUTLIER) cc_final: 0.4819 (tpt-90) REVERT: W 438 LYS cc_start: 0.8049 (ttmm) cc_final: 0.7774 (tppp) REVERT: X 37 GLU cc_start: 0.7325 (pm20) cc_final: 0.6950 (pm20) REVERT: X 94 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7533 (mt0) REVERT: X 203 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6797 (pm20) REVERT: Y 32 ASP cc_start: 0.7014 (m-30) cc_final: 0.6765 (m-30) REVERT: Y 134 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7436 (mp0) REVERT: Y 276 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7639 (ttpp) REVERT: Y 297 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: Y 300 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7183 (mtm) REVERT: Z 311 ARG cc_start: 0.8371 (mpp80) cc_final: 0.8129 (mtt-85) outliers start: 148 outliers final: 92 residues processed: 932 average time/residue: 1.5406 time to fit residues: 1647.7692 Evaluate side-chains 958 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 854 time to evaluate : 3.131 ------------------------------------------------------------------------------- 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 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 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 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 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 330 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 V residue 133 ILE Chi-restraints excluded: chain V residue 146 GLU Chi-restraints excluded: chain V residue 171 LYS 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 443 LYS Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 66 ILE 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 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 135 LEU Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 184 VAL Chi-restraints excluded: chain Y residue 193 ASP Chi-restraints excluded: chain Y residue 194 LYS 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 279 GLU Chi-restraints excluded: chain Y residue 297 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 146 optimal weight: 0.0770 chunk 187 optimal weight: 0.6980 chunk 225 optimal weight: 0.5980 chunk 147 optimal weight: 0.6980 chunk 282 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 257 optimal weight: 0.9990 chunk 197 optimal weight: 0.0570 chunk 174 optimal weight: 0.8980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1403 GLN R 146 GLN R 224 ASN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 ASN R 611 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 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 = 0.3750 r_free = 0.3750 target = 0.130838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.110490 restraints weight = 39736.583| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.98 r_work: 0.3343 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29100 Z= 0.120 Angle : 0.551 10.882 39368 Z= 0.272 Chirality : 0.043 0.185 4620 Planarity : 0.004 0.096 5039 Dihedral : 8.389 176.708 4006 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.56 % Allowed : 24.49 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3618 helix: 0.83 (0.14), residues: 1530 sheet: 0.73 (0.20), residues: 645 loop : -1.03 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 280 HIS 0.010 0.001 HIS V 27 PHE 0.022 0.001 PHE R 691 TYR 0.024 0.001 TYR X 323 ARG 0.022 0.000 ARG Q1142 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 1092) hydrogen bonds : angle 3.93684 ( 3174) covalent geometry : bond 0.00282 (29098) covalent geometry : angle 0.55070 (39368) Misc. bond : bond 0.00509 ( 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 1006 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 862 time to evaluate : 3.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.7889 (p0) cc_final: 0.7231 (p0) REVERT: Q 1139 GLU cc_start: 0.7488 (tp30) cc_final: 0.7170 (tp30) REVERT: Q 1143 VAL cc_start: 0.7905 (OUTLIER) cc_final: 0.7308 (p) REVERT: Q 1167 PHE cc_start: 0.7554 (m-10) cc_final: 0.7054 (m-80) REVERT: Q 1184 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.5717 (pp20) REVERT: Q 1302 ARG cc_start: 0.7306 (ttt180) cc_final: 0.7024 (ttt180) REVERT: Q 1321 TYR cc_start: 0.7249 (m-80) cc_final: 0.6528 (t80) REVERT: Q 1405 MET cc_start: 0.7900 (mpp) cc_final: 0.7511 (mpp) REVERT: R 74 LYS cc_start: 0.8350 (ttpp) cc_final: 0.8102 (tmmt) REVERT: R 146 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7780 (mm110) REVERT: R 676 LYS cc_start: 0.6092 (ptpt) cc_final: 0.4643 (pttt) REVERT: R 687 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7741 (mm-30) REVERT: R 736 GLU cc_start: 0.7653 (tt0) cc_final: 0.7391 (tt0) REVERT: T 241 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8348 (ttmt) REVERT: T 364 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8161 (tp) REVERT: T 431 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.8011 (mtm180) REVERT: U 66 ILE cc_start: 0.8437 (pp) cc_final: 0.8231 (mp) REVERT: U 228 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7390 (mm-30) REVERT: U 254 PHE cc_start: 0.8350 (p90) cc_final: 0.8123 (p90) REVERT: U 350 ARG cc_start: 0.8489 (mtt90) cc_final: 0.8234 (mtt-85) REVERT: V 319 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7693 (mm-30) REVERT: W 438 LYS cc_start: 0.8090 (ttmm) cc_final: 0.7775 (tppp) REVERT: X 35 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8567 (mt) REVERT: X 37 GLU cc_start: 0.7321 (pm20) cc_final: 0.6929 (pm20) REVERT: X 94 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7433 (mt0) REVERT: X 203 GLU cc_start: 0.7375 (pm20) cc_final: 0.6729 (pm20) REVERT: X 344 MET cc_start: 0.8942 (mmt) cc_final: 0.8536 (mmt) REVERT: Y 134 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7454 (mp0) REVERT: Y 157 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8025 (mptp) REVERT: Y 276 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7268 (ttpp) REVERT: Y 300 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.6999 (mtm) REVERT: Z 311 ARG cc_start: 0.8373 (mpp80) cc_final: 0.8101 (mtt180) outliers start: 144 outliers final: 84 residues processed: 922 average time/residue: 1.5460 time to fit residues: 1634.8143 Evaluate side-chains 933 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 838 time to evaluate : 3.073 ------------------------------------------------------------------------------- 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 1328 MET Chi-restraints excluded: chain Q residue 1371 LEU Chi-restraints excluded: chain Q residue 1415 ARG Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 146 GLN Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 277 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 106 VAL Chi-restraints excluded: chain T residue 134 LYS 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 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 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 283 GLU Chi-restraints excluded: chain U residue 361 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 171 LYS 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 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 234 THR Chi-restraints excluded: chain W residue 325 THR 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 206 THR Chi-restraints excluded: chain X residue 209 VAL 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 33 GLU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 42 GLU 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 157 LYS Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 229 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 246 optimal weight: 4.9990 chunk 299 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 337 optimal weight: 0.0970 chunk 56 optimal weight: 0.6980 chunk 284 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 224 optimal weight: 0.0570 chunk 300 optimal weight: 0.6980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1403 GLN R 132 ASN R 146 GLN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 ASN R 607 HIS R 611 GLN T 256 ASN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 446 GLN V 205 ASN V 394 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 Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.130900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.110649 restraints weight = 39875.960| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.86 r_work: 0.3352 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1639 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= 0.120 Angle : 0.550 10.252 39368 Z= 0.271 Chirality : 0.043 0.187 4620 Planarity : 0.004 0.087 5039 Dihedral : 8.243 175.780 4006 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.34 % Allowed : 24.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3618 helix: 0.91 (0.14), residues: 1537 sheet: 0.83 (0.20), residues: 636 loop : -0.99 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 280 HIS 0.011 0.001 HIS V 27 PHE 0.021 0.001 PHE R 691 TYR 0.026 0.001 TYR V 201 ARG 0.012 0.000 ARG Q1142 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 1092) hydrogen bonds : angle 3.91148 ( 3174) covalent geometry : bond 0.00283 (29098) covalent geometry : angle 0.54996 (39368) Misc. bond : bond 0.00499 ( 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 996 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 859 time to evaluate : 3.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.7889 (p0) cc_final: 0.7223 (p0) REVERT: Q 1139 GLU cc_start: 0.7478 (tp30) cc_final: 0.7185 (tp30) REVERT: Q 1143 VAL cc_start: 0.7827 (OUTLIER) cc_final: 0.7252 (p) REVERT: Q 1184 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5637 (pp20) REVERT: Q 1302 ARG cc_start: 0.7288 (ttt180) cc_final: 0.7014 (ttt180) REVERT: Q 1321 TYR cc_start: 0.7279 (m-80) cc_final: 0.6532 (t80) REVERT: Q 1327 MET cc_start: 0.4622 (mmm) cc_final: 0.4266 (tmm) REVERT: Q 1405 MET cc_start: 0.7862 (mpp) cc_final: 0.7458 (mtm) REVERT: R 34 TYR cc_start: 0.8206 (t80) cc_final: 0.7898 (t80) REVERT: R 74 LYS cc_start: 0.8312 (ttpp) cc_final: 0.8089 (tmmt) REVERT: R 659 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7374 (mm-40) REVERT: R 676 LYS cc_start: 0.6067 (ptpt) cc_final: 0.4479 (pttt) REVERT: R 687 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7739 (mm-30) REVERT: R 736 GLU cc_start: 0.7586 (tt0) cc_final: 0.7339 (tt0) REVERT: T 241 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8352 (ttmt) REVERT: T 364 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8156 (tp) REVERT: T 431 ARG cc_start: 0.8353 (mtm-85) cc_final: 0.8005 (mtm180) REVERT: U 228 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7424 (mm-30) REVERT: U 254 PHE cc_start: 0.8330 (p90) cc_final: 0.8128 (p90) REVERT: U 350 ARG cc_start: 0.8452 (mtt90) cc_final: 0.8206 (mtt-85) REVERT: V 319 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7674 (mm-30) REVERT: W 208 ARG cc_start: 0.5830 (OUTLIER) cc_final: 0.4829 (tpt-90) REVERT: W 220 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7182 (mpp80) REVERT: W 438 LYS cc_start: 0.8066 (ttmm) cc_final: 0.7786 (tppp) REVERT: X 35 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8554 (mt) REVERT: X 37 GLU cc_start: 0.7285 (pm20) cc_final: 0.6910 (pm20) REVERT: X 94 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7407 (mt0) REVERT: X 203 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6796 (pm20) REVERT: Y 23 HIS cc_start: 0.8486 (OUTLIER) cc_final: 0.6784 (p90) REVERT: Y 134 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7469 (mp0) REVERT: Y 157 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8035 (mptp) REVERT: Y 300 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6970 (mtm) REVERT: Z 311 ARG cc_start: 0.8363 (mpp80) cc_final: 0.8156 (mtt-85) outliers start: 137 outliers final: 85 residues processed: 914 average time/residue: 1.5158 time to fit residues: 1591.7384 Evaluate side-chains 960 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 862 time to evaluate : 3.224 ------------------------------------------------------------------------------- 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 1328 MET 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 276 VAL Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 607 HIS 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 282 GLU Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain T residue 326 LYS 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 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 171 LYS 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 418 LEU Chi-restraints excluded: chain V residue 443 LYS 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 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 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 63 ASN 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 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 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 420 VAL Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 432 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 279 optimal weight: 0.9990 chunk 222 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 327 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 246 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1403 GLN R 224 ASN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 611 GLN R 745 HIS U 62 GLN U 63 ASN U 272 GLN U 274 ASN U 310 ASN U 407 GLN U 446 GLN V 205 ASN V 394 GLN X 124 ASN 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 Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.128612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108386 restraints weight = 39655.883| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.84 r_work: 0.3311 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 29100 Z= 0.229 Angle : 0.644 12.706 39368 Z= 0.321 Chirality : 0.047 0.175 4620 Planarity : 0.004 0.094 5039 Dihedral : 8.487 179.918 4006 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.81 % Allowed : 24.97 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.14), residues: 3618 helix: 0.75 (0.14), residues: 1529 sheet: 0.67 (0.20), residues: 641 loop : -1.07 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Y 280 HIS 0.029 0.002 HIS R 607 PHE 0.019 0.002 PHE R 691 TYR 0.028 0.002 TYR X 323 ARG 0.014 0.001 ARG Q1142 Details of bonding type rmsd hydrogen bonds : bond 0.05191 ( 1092) hydrogen bonds : angle 4.10959 ( 3174) covalent geometry : bond 0.00558 (29098) covalent geometry : angle 0.64426 (39368) Misc. bond : bond 0.00720 ( 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 1028 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 876 time to evaluate : 3.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.8141 (p0) cc_final: 0.7206 (p0) REVERT: Q 1139 GLU cc_start: 0.7448 (tp30) cc_final: 0.7188 (tp30) REVERT: Q 1143 VAL cc_start: 0.7964 (OUTLIER) cc_final: 0.7358 (p) REVERT: Q 1184 GLU cc_start: 0.6031 (OUTLIER) cc_final: 0.5715 (pp20) REVERT: Q 1302 ARG cc_start: 0.7293 (ttt180) cc_final: 0.7020 (ttt180) REVERT: Q 1321 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.6580 (t80) REVERT: Q 1405 MET cc_start: 0.7980 (mpp) cc_final: 0.7542 (mpp) REVERT: R 74 LYS cc_start: 0.8363 (ttpp) cc_final: 0.8120 (tmmt) REVERT: R 84 ASN cc_start: 0.8546 (m110) cc_final: 0.8312 (m110) REVERT: R 152 GLN cc_start: 0.7402 (tm-30) cc_final: 0.6849 (tm-30) REVERT: R 245 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8157 (t) REVERT: R 263 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8519 (ptmm) REVERT: R 659 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7498 (mm-40) REVERT: R 676 LYS cc_start: 0.6056 (ptpt) cc_final: 0.4252 (ptpp) REVERT: R 687 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7807 (mm-30) REVERT: R 736 GLU cc_start: 0.7624 (tt0) cc_final: 0.7353 (tt0) REVERT: S 80 LYS cc_start: 0.8565 (tppt) cc_final: 0.8308 (tppt) REVERT: T 241 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8342 (ttmt) REVERT: T 364 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8172 (tp) REVERT: T 431 ARG cc_start: 0.8367 (mtm-85) cc_final: 0.8032 (mtm180) REVERT: T 456 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8374 (mp) REVERT: U 350 ARG cc_start: 0.8546 (mtt90) cc_final: 0.8263 (mtt-85) REVERT: V 418 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8648 (mp) REVERT: W 38 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8298 (mtt180) REVERT: W 208 ARG cc_start: 0.5817 (OUTLIER) cc_final: 0.4765 (tpt-90) REVERT: W 438 LYS cc_start: 0.8108 (ttmm) cc_final: 0.7761 (tppp) REVERT: X 37 GLU cc_start: 0.7356 (pm20) cc_final: 0.6973 (pm20) REVERT: X 94 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7486 (mt0) REVERT: X 203 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6842 (pm20) REVERT: Y 23 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.6799 (p90) REVERT: Y 32 ASP cc_start: 0.7022 (m-30) cc_final: 0.6773 (m-30) REVERT: Y 134 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7416 (mp0) REVERT: Y 157 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8167 (mptp) REVERT: Y 300 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7605 (mtm) REVERT: Y 374 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7276 (tm-30) REVERT: Z 311 ARG cc_start: 0.8366 (mpp80) cc_final: 0.8104 (mtt-85) outliers start: 152 outliers final: 93 residues processed: 941 average time/residue: 1.5036 time to fit residues: 1630.7438 Evaluate side-chains 969 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 860 time to evaluate : 3.162 ------------------------------------------------------------------------------- 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 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 1221 ILE Chi-restraints excluded: chain Q residue 1321 TYR Chi-restraints excluded: chain Q residue 1328 MET 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 145 SER Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 263 LYS Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 607 HIS 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 90 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 134 LYS 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 282 GLU Chi-restraints excluded: chain T residue 294 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 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 T residue 456 LEU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 59 LYS 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 289 VAL 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 450 ASP Chi-restraints excluded: chain V residue 146 GLU Chi-restraints excluded: chain V residue 171 LYS 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 418 LEU Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 132 GLU Chi-restraints excluded: chain W residue 174 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 251 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 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 71 VAL Chi-restraints excluded: chain Y residue 84 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 200 THR Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 285 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 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 199 optimal weight: 0.9980 chunk 265 optimal weight: 0.9990 chunk 336 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 239 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 254 optimal weight: 0.9990 chunk 287 optimal weight: 0.3980 chunk 110 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 U 63 ASN U 230 GLN U 274 ASN U 310 ASN V 205 ASN V 325 ASN X 256 ASN X 289 ASN X 325 ASN X 440 ASN Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 443 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.129262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109084 restraints weight = 39907.839| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.85 r_work: 0.3325 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29100 Z= 0.183 Angle : 0.617 15.173 39368 Z= 0.306 Chirality : 0.045 0.208 4620 Planarity : 0.004 0.106 5039 Dihedral : 8.451 177.249 4006 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.18 % Allowed : 25.60 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3618 helix: 0.72 (0.13), residues: 1535 sheet: 0.65 (0.20), residues: 641 loop : -1.05 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Y 280 HIS 0.008 0.001 HIS V 27 PHE 0.021 0.002 PHE R 691 TYR 0.029 0.002 TYR R 34 ARG 0.025 0.001 ARG Q1142 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 1092) hydrogen bonds : angle 4.07712 ( 3174) covalent geometry : bond 0.00446 (29098) covalent geometry : angle 0.61680 (39368) Misc. bond : bond 0.00689 ( 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 984 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 852 time to evaluate : 3.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.8081 (p0) cc_final: 0.7226 (p0) REVERT: Q 1139 GLU cc_start: 0.7512 (tp30) cc_final: 0.7209 (tp30) REVERT: Q 1143 VAL cc_start: 0.7849 (OUTLIER) cc_final: 0.7216 (p) REVERT: Q 1184 GLU cc_start: 0.6022 (OUTLIER) cc_final: 0.5706 (pp20) REVERT: Q 1302 ARG cc_start: 0.7289 (ttt180) cc_final: 0.7014 (ttt180) REVERT: Q 1321 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.6561 (t80) REVERT: Q 1327 MET cc_start: 0.4530 (tmm) cc_final: 0.4240 (tmm) REVERT: Q 1405 MET cc_start: 0.7972 (mpp) cc_final: 0.7518 (mpp) REVERT: R 74 LYS cc_start: 0.8363 (ttpp) cc_final: 0.8123 (tmmt) REVERT: R 263 LYS cc_start: 0.8735 (ptmm) cc_final: 0.8531 (ptmm) REVERT: R 659 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7456 (mm-40) REVERT: R 676 LYS cc_start: 0.6037 (ptpt) cc_final: 0.4270 (ptpp) REVERT: R 687 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7795 (mm-30) REVERT: R 736 GLU cc_start: 0.7600 (tt0) cc_final: 0.7331 (tt0) REVERT: T 241 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8367 (ttmt) REVERT: T 364 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8184 (tp) REVERT: T 431 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.8024 (mtm180) REVERT: T 456 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8370 (mp) REVERT: U 230 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7736 (tp40) REVERT: U 254 PHE cc_start: 0.8317 (p90) cc_final: 0.8084 (p90) REVERT: U 350 ARG cc_start: 0.8510 (mtt90) cc_final: 0.8226 (mtt-85) REVERT: V 325 ASN cc_start: 0.8137 (m-40) cc_final: 0.7935 (m-40) REVERT: V 394 GLN cc_start: 0.8408 (mt0) cc_final: 0.8127 (mt0) REVERT: W 208 ARG cc_start: 0.5796 (OUTLIER) cc_final: 0.4739 (tpt-90) REVERT: W 220 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7148 (mpp80) REVERT: W 438 LYS cc_start: 0.8050 (ttmm) cc_final: 0.7780 (tppp) REVERT: X 37 GLU cc_start: 0.7348 (pm20) cc_final: 0.6957 (pm20) REVERT: X 94 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7474 (mt0) REVERT: X 203 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6810 (pm20) REVERT: X 344 MET cc_start: 0.8943 (mmt) cc_final: 0.8629 (mmt) REVERT: Y 23 HIS cc_start: 0.8562 (OUTLIER) cc_final: 0.6816 (p90) REVERT: Y 134 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7430 (mp0) REVERT: Y 157 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7948 (mtpt) REVERT: Y 297 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: Y 300 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7450 (mtm) REVERT: Y 374 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7300 (tm-30) REVERT: Z 311 ARG cc_start: 0.8358 (mpp80) cc_final: 0.8028 (mtt-85) outliers start: 132 outliers final: 92 residues processed: 907 average time/residue: 1.5511 time to fit residues: 1613.0855 Evaluate side-chains 961 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 854 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL 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 1221 ILE Chi-restraints excluded: chain Q residue 1321 TYR Chi-restraints excluded: chain Q residue 1328 MET 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 144 GLN Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 703 SER Chi-restraints excluded: chain S residue 49 LYS 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 150 GLU Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 181 LEU Chi-restraints excluded: chain T residue 206 THR 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 294 LYS Chi-restraints excluded: chain T residue 326 LYS 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 59 LYS 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 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 146 GLU Chi-restraints excluded: chain V residue 171 LYS 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 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 W residue 424 LYS 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 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 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 157 LYS Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 179 LEU Chi-restraints excluded: chain Y residue 185 LEU 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 235 VAL Chi-restraints excluded: chain Y residue 285 LYS Chi-restraints excluded: chain Y residue 297 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 286 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 338 optimal weight: 0.8980 chunk 333 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 341 optimal weight: 0.0870 chunk 57 optimal weight: 0.5980 chunk 258 optimal weight: 1.9990 chunk 124 optimal weight: 0.0570 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1207 GLN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 611 GLN R 745 HIS T 256 ASN U 63 ASN U 274 ASN U 310 ASN V 205 ASN W 310 ASN X 256 ASN X 289 ASN X 325 ASN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110413 restraints weight = 39662.098| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.85 r_work: 0.3344 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29100 Z= 0.129 Angle : 0.586 12.274 39368 Z= 0.290 Chirality : 0.043 0.183 4620 Planarity : 0.004 0.102 5039 Dihedral : 8.283 174.564 4006 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.54 % Allowed : 26.27 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3618 helix: 0.81 (0.14), residues: 1544 sheet: 0.63 (0.20), residues: 670 loop : -0.99 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Y 280 HIS 0.007 0.001 HIS V 27 PHE 0.023 0.001 PHE R 691 TYR 0.029 0.001 TYR R 34 ARG 0.015 0.000 ARG Q1142 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 1092) hydrogen bonds : angle 3.99255 ( 3174) covalent geometry : bond 0.00308 (29098) covalent geometry : angle 0.58577 (39368) Misc. bond : bond 0.00567 ( 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 961 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 849 time to evaluate : 3.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.7992 (p0) cc_final: 0.7213 (p0) REVERT: Q 1139 GLU cc_start: 0.7506 (tp30) cc_final: 0.7197 (tp30) REVERT: Q 1143 VAL cc_start: 0.7755 (OUTLIER) cc_final: 0.7141 (p) REVERT: Q 1184 GLU cc_start: 0.6043 (OUTLIER) cc_final: 0.5724 (pp20) REVERT: Q 1302 ARG cc_start: 0.7286 (ttt180) cc_final: 0.7008 (ttt180) REVERT: Q 1321 TYR cc_start: 0.7275 (m-80) cc_final: 0.6512 (t80) REVERT: Q 1405 MET cc_start: 0.7961 (mpp) cc_final: 0.7499 (mpp) REVERT: R 34 TYR cc_start: 0.8137 (t80) cc_final: 0.7886 (t80) REVERT: R 74 LYS cc_start: 0.8357 (ttpp) cc_final: 0.8113 (tmmt) REVERT: R 90 GLN cc_start: 0.7511 (tp-100) cc_final: 0.7199 (tp-100) REVERT: R 263 LYS cc_start: 0.8717 (ptmm) cc_final: 0.8487 (ptmm) REVERT: R 659 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7462 (mm-40) REVERT: R 676 LYS cc_start: 0.6020 (ptpt) cc_final: 0.4301 (ptpp) REVERT: R 687 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7754 (mm-30) REVERT: R 736 GLU cc_start: 0.7558 (tt0) cc_final: 0.7294 (tt0) REVERT: T 241 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8375 (ttmt) REVERT: T 285 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7916 (mtt90) REVERT: T 431 ARG cc_start: 0.8340 (mtm-85) cc_final: 0.8004 (mtm180) REVERT: T 456 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8402 (mp) REVERT: U 228 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7543 (mm-30) REVERT: U 254 PHE cc_start: 0.8305 (p90) cc_final: 0.8042 (p90) REVERT: U 350 ARG cc_start: 0.8480 (mtt90) cc_final: 0.8217 (mtt-85) REVERT: U 450 ASP cc_start: 0.7818 (m-30) cc_final: 0.7545 (m-30) REVERT: V 412 LEU cc_start: 0.8303 (tp) cc_final: 0.8093 (tp) REVERT: V 433 GLU cc_start: 0.7083 (tp30) cc_final: 0.6694 (tm-30) REVERT: W 208 ARG cc_start: 0.5778 (OUTLIER) cc_final: 0.4660 (tpt-90) REVERT: W 220 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7128 (mpp80) REVERT: W 438 LYS cc_start: 0.8021 (ttmm) cc_final: 0.7781 (tppp) REVERT: X 37 GLU cc_start: 0.7331 (pm20) cc_final: 0.6930 (pm20) REVERT: X 94 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7454 (mt0) REVERT: X 180 ARG cc_start: 0.8058 (mtp85) cc_final: 0.7510 (mtp180) REVERT: X 203 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6776 (pm20) REVERT: X 344 MET cc_start: 0.8936 (mmt) cc_final: 0.8707 (mmt) REVERT: Y 23 HIS cc_start: 0.8525 (OUTLIER) cc_final: 0.6703 (p90) REVERT: Y 32 ASP cc_start: 0.6988 (m-30) cc_final: 0.6763 (m-30) REVERT: Y 134 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7450 (mp0) REVERT: Y 157 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8093 (mptp) REVERT: Y 276 LYS cc_start: 0.8418 (tppp) cc_final: 0.8212 (tttp) REVERT: Y 300 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7217 (mtm) REVERT: Z 311 ARG cc_start: 0.8373 (mpp80) cc_final: 0.8113 (mtt180) outliers start: 112 outliers final: 80 residues processed: 901 average time/residue: 1.5573 time to fit residues: 1620.5087 Evaluate side-chains 940 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 848 time to evaluate : 3.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL 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 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 276 VAL Chi-restraints excluded: chain R residue 277 VAL 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 150 GLU Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 181 LEU 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 285 ARG Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 363 LEU 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 289 VAL 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 171 LYS Chi-restraints excluded: chain V residue 190 GLN Chi-restraints excluded: chain V residue 286 GLN 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 W residue 423 VAL Chi-restraints excluded: chain W residue 424 LYS 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 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 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 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 229 LEU Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 285 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 87 optimal weight: 3.9990 chunk 18 optimal weight: 0.0570 chunk 322 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1207 GLN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 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 23 HIS ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.129833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109627 restraints weight = 39729.256| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.85 r_work: 0.3333 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1884 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= 0.160 Angle : 0.606 11.310 39368 Z= 0.301 Chirality : 0.045 0.189 4620 Planarity : 0.004 0.105 5039 Dihedral : 8.296 173.660 4006 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.16 % Allowed : 26.90 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3618 helix: 0.76 (0.13), residues: 1543 sheet: 0.60 (0.20), residues: 659 loop : -0.99 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP Y 280 HIS 0.011 0.001 HIS V 27 PHE 0.026 0.001 PHE Q1274 TYR 0.029 0.002 TYR R 34 ARG 0.015 0.000 ARG Q1142 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 1092) hydrogen bonds : angle 4.02652 ( 3174) covalent geometry : bond 0.00386 (29098) covalent geometry : angle 0.60630 (39368) Misc. bond : bond 0.00610 ( 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 952 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 852 time to evaluate : 3.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1103 ASP cc_start: 0.7993 (p0) cc_final: 0.7218 (p0) REVERT: Q 1139 GLU cc_start: 0.7498 (tp30) cc_final: 0.7204 (tp30) REVERT: Q 1143 VAL cc_start: 0.7781 (OUTLIER) cc_final: 0.7194 (p) REVERT: Q 1167 PHE cc_start: 0.7545 (m-80) cc_final: 0.7299 (m-10) REVERT: Q 1184 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5704 (pp20) REVERT: Q 1302 ARG cc_start: 0.7293 (ttt180) cc_final: 0.7012 (ttt180) REVERT: Q 1321 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.6554 (t80) REVERT: Q 1327 MET cc_start: 0.4515 (mmm) cc_final: 0.4182 (tmm) REVERT: Q 1405 MET cc_start: 0.8010 (mpp) cc_final: 0.7544 (mpp) REVERT: R 74 LYS cc_start: 0.8358 (ttpp) cc_final: 0.8093 (tmmt) REVERT: R 90 GLN cc_start: 0.7509 (tp-100) cc_final: 0.7199 (tp-100) REVERT: R 263 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8480 (ptmm) REVERT: R 659 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7501 (mm-40) REVERT: R 676 LYS cc_start: 0.6068 (ptpt) cc_final: 0.4300 (ptpp) REVERT: R 687 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7798 (mm-30) REVERT: R 719 ARG cc_start: 0.7741 (mpp80) cc_final: 0.7185 (mpp-170) REVERT: R 736 GLU cc_start: 0.7591 (tt0) cc_final: 0.7317 (tt0) REVERT: T 241 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8412 (ttmt) REVERT: T 431 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.8017 (mtm180) REVERT: T 456 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8367 (mp) REVERT: U 228 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7407 (mm-30) REVERT: U 350 ARG cc_start: 0.8481 (mtt90) cc_final: 0.8205 (mtt-85) REVERT: V 412 LEU cc_start: 0.8289 (tp) cc_final: 0.8080 (tp) REVERT: V 433 GLU cc_start: 0.7079 (tp30) cc_final: 0.6672 (mm-30) REVERT: W 208 ARG cc_start: 0.5812 (OUTLIER) cc_final: 0.4700 (tpt-90) REVERT: W 220 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7117 (mpp80) REVERT: W 438 LYS cc_start: 0.8005 (ttmm) cc_final: 0.7766 (tppp) REVERT: X 37 GLU cc_start: 0.7349 (pm20) cc_final: 0.6965 (pm20) REVERT: X 94 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7486 (mt0) REVERT: X 203 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6774 (pm20) REVERT: X 344 MET cc_start: 0.8924 (mmt) cc_final: 0.8695 (mmt) REVERT: Y 23 HIS cc_start: 0.8574 (OUTLIER) cc_final: 0.7263 (p-80) REVERT: Y 32 ASP cc_start: 0.7021 (m-30) cc_final: 0.6777 (m-30) REVERT: Y 134 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7452 (mp0) REVERT: Y 157 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8133 (mptp) REVERT: Y 279 GLU cc_start: 0.8316 (pt0) cc_final: 0.8108 (pt0) REVERT: Y 300 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7359 (mtm) REVERT: Y 374 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7368 (tm-30) REVERT: Z 311 ARG cc_start: 0.8367 (mpp80) cc_final: 0.8078 (mtm-85) outliers start: 100 outliers final: 76 residues processed: 897 average time/residue: 1.6039 time to fit residues: 1647.3854 Evaluate side-chains 938 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 849 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1022 VAL 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 145 SER Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 263 LYS Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain R residue 277 VAL 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 150 GLU Chi-restraints excluded: chain T residue 166 VAL Chi-restraints excluded: chain T residue 181 LEU 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 294 LYS Chi-restraints excluded: chain T residue 326 LYS 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 289 VAL Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 171 LYS 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 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 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 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 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 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 235 VAL Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 285 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 206 optimal weight: 0.6980 chunk 121 optimal weight: 0.0270 chunk 285 optimal weight: 2.9990 chunk 91 optimal weight: 0.0270 chunk 324 optimal weight: 0.1980 chunk 346 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 142 optimal weight: 1.9990 chunk 312 optimal weight: 0.5980 chunk 3 optimal weight: 20.0000 chunk 20 optimal weight: 0.6980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1207 GLN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 611 GLN R 745 HIS T 256 ASN U 63 ASN U 274 ASN U 310 ASN V 205 ASN W 310 ASN X 256 ASN X 289 ASN X 314 ASN Y 23 HIS Y 223 GLN ** Y 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 310 ASN Y 443 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.131542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111445 restraints weight = 39672.065| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.86 r_work: 0.3364 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29100 Z= 0.109 Angle : 0.571 12.311 39368 Z= 0.282 Chirality : 0.043 0.174 4620 Planarity : 0.004 0.082 5039 Dihedral : 8.035 171.019 4006 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.82 % Allowed : 27.50 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3618 helix: 0.90 (0.14), residues: 1544 sheet: 0.70 (0.20), residues: 668 loop : -0.94 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP Y 280 HIS 0.015 0.001 HIS Y 23 PHE 0.023 0.001 PHE R 691 TYR 0.030 0.001 TYR R 34 ARG 0.012 0.000 ARG Q1142 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 1092) hydrogen bonds : angle 3.92606 ( 3174) covalent geometry : bond 0.00254 (29098) covalent geometry : angle 0.57056 (39368) Misc. bond : bond 0.00435 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32024.30 seconds wall clock time: 548 minutes 58.47 seconds (32938.47 seconds total)