Starting phenix.real_space_refine on Mon May 26 23:48:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8etu_28599/05_2025/8etu_28599.cif Found real_map, /net/cci-nas-00/data/ceres_data/8etu_28599/05_2025/8etu_28599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8etu_28599/05_2025/8etu_28599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8etu_28599/05_2025/8etu_28599.map" model { file = "/net/cci-nas-00/data/ceres_data/8etu_28599/05_2025/8etu_28599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8etu_28599/05_2025/8etu_28599.cif" } resolution = 2.8 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 95 5.16 5 C 18041 2.51 5 N 4942 2.21 5 O 5580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 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: 28670 Number of models: 1 Model: "" Number of chains: 16 Chain: "R" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3548 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain breaks: 1 Chain: "S" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1014 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 9, 'TRANS': 115} Chain breaks: 1 Chain: "T" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3339 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3354 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3404 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 18, 'TRANS': 424} Chain: "W" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3398 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 431} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "Y" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3421 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 434} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "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: "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: 16.89, per 1000 atoms: 0.59 Number of scatterers: 28670 At special positions: 0 Unit cell: (132.765, 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 5580 8.00 N 4942 7.00 C 18041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.81 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: 150 helices and 35 sheets defined 43.9% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain 'R' and resid 30 through 34 removed outlier: 3.660A pdb=" N ALA R 33 " --> pdb=" O GLU R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 87 Processing helix chain 'R' and resid 89 through 95 Processing helix chain 'R' and resid 108 through 122 Processing helix chain 'R' and resid 143 through 158 removed outlier: 3.867A pdb=" N ARG R 147 " --> pdb=" O VAL R 143 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU R 156 " --> pdb=" O GLN R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 177 Processing helix chain 'R' and resid 215 through 231 removed outlier: 3.549A pdb=" N TYR R 231 " --> pdb=" O MET R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 250 removed outlier: 3.534A pdb=" N TYR R 243 " --> pdb=" O SER R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 262 removed outlier: 3.873A pdb=" N GLU R 262 " --> pdb=" O ASP R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 585 through 588 removed outlier: 3.671A pdb=" N ASN R 588 " --> pdb=" O ASP R 585 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 585 through 588' Processing helix chain 'R' and resid 589 through 597 Processing helix chain 'R' and resid 607 through 609 No H-bonds generated for 'chain 'R' and resid 607 through 609' Processing helix chain 'R' and resid 616 through 621 Processing helix chain 'R' and resid 622 through 626 removed outlier: 3.921A pdb=" N ILE R 625 " --> pdb=" O PRO R 622 " (cutoff:3.500A) Processing helix chain 'R' and resid 627 through 631 Processing helix chain 'R' and resid 637 through 649 removed outlier: 3.606A pdb=" N LYS R 649 " --> pdb=" O ILE R 645 " (cutoff:3.500A) Processing helix chain 'R' and resid 658 through 666 Processing helix chain 'R' and resid 672 through 676 removed outlier: 3.557A pdb=" N ALA R 675 " --> pdb=" O GLY R 672 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS R 676 " --> pdb=" O GLY R 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 672 through 676' Processing helix chain 'R' and resid 679 through 692 Processing helix chain 'R' and resid 708 through 720 Processing helix chain 'R' and resid 720 through 725 removed outlier: 3.552A pdb=" N TYR R 724 " --> pdb=" O ASN R 720 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG R 725 " --> pdb=" O GLU R 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 720 through 725' Processing helix chain 'R' and resid 731 through 738 Processing helix chain 'S' and resid 31 through 38 removed outlier: 3.971A pdb=" N SER S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 83 removed outlier: 3.691A pdb=" N LEU S 66 " --> pdb=" O SER S 62 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE S 67 " --> pdb=" O ALA S 63 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER S 68 " --> pdb=" O ARG S 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS S 83 " --> pdb=" O THR S 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'S' and resid 151 through 158 removed outlier: 3.965A pdb=" N LEU S 158 " --> pdb=" O GLU S 154 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 68 removed outlier: 3.816A 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: 3.638A 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: 3.591A 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: 3.763A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) Processing helix chain 'T' and resid 360 through 365 removed outlier: 3.755A pdb=" N ASP T 365 " --> pdb=" O PRO T 361 " (cutoff:3.500A) Processing helix chain 'T' and resid 376 through 391 Processing helix chain 'T' and resid 396 through 410 Processing helix chain 'T' and resid 411 through 429 removed outlier: 4.118A pdb=" N ALA T 415 " --> pdb=" O SER T 411 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU T 416 " --> pdb=" O LEU T 412 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ALA T 420 " --> pdb=" O LEU T 416 " (cutoff:3.500A) Proline residue: T 421 - end of helix removed outlier: 3.531A 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 80 through 93 removed outlier: 3.676A 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: 4.054A pdb=" N ARG U 270 " --> pdb=" O ARG U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 298 through 301 Processing helix chain 'U' and resid 302 through 313 removed outlier: 3.582A pdb=" N ARG U 311 " --> pdb=" O SER U 307 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU U 313 " --> pdb=" O ILE U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 344 through 349 Processing helix chain 'U' and resid 360 through 375 Processing helix chain 'U' and resid 380 through 394 Processing helix chain 'U' and resid 395 through 413 removed outlier: 3.595A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL U 405 " --> pdb=" O ASN U 401 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN U 407 " --> pdb=" O ILE U 403 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE U 409 " --> pdb=" O VAL U 405 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG U 413 " --> pdb=" O ILE U 409 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 removed outlier: 3.547A pdb=" N VAL U 423 " --> pdb=" O GLU U 419 " (cutoff:3.500A) Processing helix chain 'U' and resid 432 through 442 removed outlier: 3.770A pdb=" N GLU U 442 " --> pdb=" O LYS U 438 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 68 removed outlier: 3.895A pdb=" N LYS V 68 " --> pdb=" O LEU V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 97 Processing helix chain 'V' and resid 108 through 111 removed outlier: 3.750A pdb=" N TYR V 111 " --> pdb=" O SER V 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 108 through 111' Processing helix chain 'V' and resid 116 through 128 Processing helix chain 'V' and resid 182 through 192 removed outlier: 3.677A pdb=" N TYR V 186 " --> pdb=" O ASP V 182 " (cutoff:3.500A) removed outlier: 3.691A 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 273 removed outlier: 3.548A pdb=" N GLN V 271 " --> pdb=" O SER V 267 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU V 272 " --> pdb=" O MET V 268 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU V 273 " --> pdb=" O MET V 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 298 removed outlier: 3.589A 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: 3.727A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) Processing helix chain 'V' and resid 360 through 365 removed outlier: 3.705A pdb=" N ASP V 365 " --> pdb=" O PRO V 361 " (cutoff:3.500A) Processing helix chain 'V' and resid 376 through 391 Processing helix chain 'V' and resid 396 through 410 Processing helix chain 'V' and resid 411 through 417 Processing helix chain 'V' and resid 418 through 428 Processing helix chain 'V' and resid 435 through 446 Processing helix chain 'V' and resid 448 through 458 removed outlier: 3.516A pdb=" N THR V 458 " --> pdb=" O LYS V 454 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 64 removed outlier: 3.737A pdb=" N GLY W 64 " --> pdb=" O MET W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 93 removed outlier: 3.960A 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: 4.313A pdb=" N ARG W 250 " --> pdb=" O VAL W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 252 through 260 removed outlier: 3.577A pdb=" N ALA W 256 " --> pdb=" O GLN W 252 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE W 258 " --> pdb=" O PHE W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 284 removed outlier: 3.736A pdb=" N ARG W 270 " --> pdb=" O ARG W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 313 removed outlier: 3.865A 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: 3.693A pdb=" N ARG W 350 " --> pdb=" O ASP W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 375 Processing helix chain 'W' and resid 380 through 394 Processing helix chain 'W' and resid 395 through 411 removed outlier: 3.795A pdb=" N SER W 399 " --> pdb=" O SER W 395 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) Processing helix chain 'W' and resid 412 through 414 No H-bonds generated for 'chain 'W' and resid 412 through 414' Processing helix chain 'W' and resid 419 through 430 removed outlier: 3.525A pdb=" N VAL W 423 " --> pdb=" O GLU W 419 " (cutoff:3.500A) Processing helix chain 'W' and resid 432 through 442 removed outlier: 3.706A pdb=" N GLU W 442 " --> pdb=" O LYS W 438 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 68 removed outlier: 3.811A pdb=" N LYS X 68 " --> pdb=" O LEU X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 97 Processing helix chain 'X' and resid 108 through 111 removed outlier: 3.770A 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 Processing helix chain 'X' and resid 264 through 272 removed outlier: 3.684A pdb=" N MET X 268 " --> pdb=" O ASP X 264 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 298 removed outlier: 3.724A pdb=" N ARG X 285 " --> pdb=" O THR X 281 " (cutoff:3.500A) Processing helix chain 'X' and resid 312 through 316 removed outlier: 3.578A pdb=" N MET X 315 " --> pdb=" O GLU X 312 " (cutoff:3.500A) Processing helix chain 'X' and resid 317 through 328 Processing helix chain 'X' and resid 360 through 365 removed outlier: 3.571A pdb=" N ASP X 365 " --> pdb=" O PRO X 361 " (cutoff:3.500A) 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 Processing helix chain 'X' and resid 435 through 446 Processing helix chain 'X' and resid 448 through 458 Processing helix chain 'Y' and resid 49 through 64 removed outlier: 3.524A pdb=" N GLY Y 64 " --> pdb=" O MET Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 80 through 93 removed outlier: 4.098A pdb=" N GLY Y 93 " --> pdb=" O SER Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'Y' and resid 172 through 181 removed outlier: 3.546A 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: 3.748A pdb=" N ARG Y 270 " --> pdb=" O ARG Y 266 " (cutoff:3.500A) Processing helix chain 'Y' and resid 302 through 312 Processing helix chain 'Y' and resid 344 through 350 removed outlier: 3.591A 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: 3.879A pdb=" N SER Y 399 " --> pdb=" O SER Y 395 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 removed outlier: 3.534A pdb=" N VAL Y 423 " --> pdb=" O GLU Y 419 " (cutoff:3.500A) Processing helix chain 'Y' and resid 432 through 442 Processing helix chain 'Y' and resid 443 through 447 removed outlier: 3.660A pdb=" N TYR Y 447 " --> pdb=" O GLU Y 444 " (cutoff:3.500A) Processing helix chain 'Q' and resid 957 through 971 removed outlier: 3.621A pdb=" N ILE Q 971 " --> pdb=" O LEU Q 967 " (cutoff:3.500A) Processing helix chain 'Q' and resid 974 through 985 Processing helix chain 'Q' and resid 1000 through 1013 removed outlier: 3.780A pdb=" N GLN Q1006 " --> pdb=" O ASN Q1002 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE Q1007 " --> pdb=" O ALA Q1003 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1013 through 1018 removed outlier: 3.960A pdb=" N PHE Q1017 " --> pdb=" O HIS Q1013 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1086 through 1094 removed outlier: 3.857A pdb=" N TYR Q1090 " --> pdb=" O PRO Q1086 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1101 through 1111 Processing helix chain 'Q' and resid 1121 through 1133 Processing helix chain 'Q' and resid 1138 through 1144 Processing helix chain 'Q' and resid 1147 through 1154 Processing helix chain 'Q' and resid 1169 through 1176 Processing helix chain 'Q' and resid 1177 through 1180 removed outlier: 4.328A pdb=" N ASN Q1180 " --> pdb=" O VAL Q1177 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1177 through 1180' Processing helix chain 'Q' and resid 1185 through 1191 Processing helix chain 'Q' and resid 1192 through 1201 removed outlier: 3.604A pdb=" N HIS Q1196 " --> pdb=" O ASN Q1192 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU Q1201 " --> pdb=" O ALA Q1197 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1226 through 1238 removed outlier: 3.872A pdb=" N THR Q1230 " --> pdb=" O SER Q1226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1239 through 1246 Processing helix chain 'Q' and resid 1250 through 1259 Processing helix chain 'Q' and resid 1264 through 1268 Processing helix chain 'Q' and resid 1280 through 1284 removed outlier: 3.792A pdb=" N SER Q1283 " --> pdb=" O LYS Q1280 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER Q1284 " --> pdb=" O ASN Q1281 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1280 through 1284' Processing helix chain 'Q' and resid 1292 through 1298 removed outlier: 3.568A pdb=" N THR Q1296 " --> pdb=" O ASP Q1292 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER Q1298 " --> pdb=" O PHE Q1294 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1298 through 1315 removed outlier: 4.362A pdb=" N VAL Q1309 " --> pdb=" O ASP Q1305 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LYS Q1310 " --> pdb=" O GLU Q1306 " (cutoff:3.500A) removed outlier: 3.679A 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: 3.854A pdb=" N ALA Q1408 " --> pdb=" O ALA Q1404 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1427 through 1432 removed outlier: 3.880A pdb=" N ARG Q1431 " --> pdb=" O THR Q1427 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 14 through 15 removed outlier: 3.535A pdb=" N VAL R 14 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 61 through 64 removed outlier: 6.835A pdb=" N ILE R 40 " --> pdb=" O LEU R 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 67 through 71 Processing sheet with id=AA4, first strand: chain 'R' and resid 100 through 101 removed outlier: 3.759A pdb=" N PHE R 104 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 162 through 163 Processing sheet with id=AA6, 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=AA7, first strand: chain 'S' and resid 125 through 126 Processing sheet with id=AA8, first strand: chain 'T' and resid 102 through 106 removed outlier: 6.311A pdb=" N CYS T 103 " --> pdb=" O PHE T 309 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ASP T 311 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU T 105 " --> pdb=" O ASP T 311 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE T 75 " --> pdb=" O LEU T 338 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N SER T 340 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU T 77 " --> pdb=" O SER T 340 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ALA T 74 " --> pdb=" O LEU T 368 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL T 370 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU T 76 " --> pdb=" O VAL T 370 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 129 through 151 removed outlier: 6.265A pdb=" N GLY T 169 " --> pdb=" O THR T 145 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU T 147 " --> pdb=" O ILE T 167 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE T 167 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N HIS T 165 " --> pdb=" O PRO T 149 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASP T 151 " --> pdb=" O ILE T 163 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE T 163 " --> pdb=" O ASP T 151 " (cutoff:3.500A) removed outlier: 3.667A 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: 6.519A pdb=" N VAL T 230 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ARG T 214 " --> pdb=" O VAL T 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 344 through 346 Processing sheet with id=AB2, first strand: chain 'T' and resid 394 through 395 removed outlier: 7.173A pdb=" N GLN T 394 " --> pdb=" O ILE T 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'U' and resid 40 through 41 Processing sheet with id=AB4, first strand: chain 'U' and resid 98 through 102 removed outlier: 6.357A pdb=" N THR U 99 " --> pdb=" O PHE U 294 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASP U 296 " --> pdb=" O THR U 99 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE U 101 " --> pdb=" O ASP U 296 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'U' and resid 125 through 147 removed outlier: 6.730A pdb=" N THR U 159 " --> pdb=" O VAL U 141 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE U 143 " --> pdb=" O LYS U 157 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS U 157 " --> pdb=" O ILE U 143 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE U 145 " --> pdb=" O GLN U 155 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLN U 155 " --> pdb=" O ILE U 145 " (cutoff:3.500A) removed outlier: 4.139A 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=AB6, first strand: chain 'U' and resid 329 through 331 Processing sheet with id=AB7, first strand: chain 'V' and resid 44 through 45 removed outlier: 3.548A pdb=" N GLU V 45 " --> pdb=" O PHE V 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'V' and resid 102 through 106 removed outlier: 6.325A pdb=" N CYS V 103 " --> pdb=" O PHE V 309 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASP V 311 " --> pdb=" O CYS V 103 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU V 105 " --> pdb=" O ASP V 311 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU V 308 " --> pdb=" O VAL V 337 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ALA V 339 " --> pdb=" O LEU V 308 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE V 310 " --> pdb=" O ALA V 339 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA V 74 " --> pdb=" O LEU V 368 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL V 370 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU V 76 " --> pdb=" O VAL V 370 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'V' and resid 129 through 151 removed outlier: 6.515A pdb=" N GLY V 169 " --> pdb=" O THR V 145 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU V 147 " --> pdb=" O ILE V 167 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE V 167 " --> pdb=" O LEU V 147 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N HIS V 165 " --> pdb=" O PRO V 149 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP V 151 " --> pdb=" O ILE V 163 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE V 163 " --> pdb=" O ASP V 151 " (cutoff:3.500A) removed outlier: 3.700A 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: 6.496A pdb=" N VAL V 230 " --> pdb=" O VAL V 212 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ARG V 214 " --> pdb=" O VAL V 230 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'V' and resid 344 through 346 Processing sheet with id=AC2, first strand: chain 'W' and resid 40 through 41 Processing sheet with id=AC3, first strand: chain 'W' and resid 98 through 102 removed outlier: 6.398A pdb=" N THR W 99 " --> pdb=" O PHE W 294 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ASP W 296 " --> pdb=" O THR W 99 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE W 101 " --> pdb=" O ASP W 296 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU W 293 " --> pdb=" O MET W 322 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ALA W 324 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE W 295 " --> pdb=" O ALA W 324 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'W' and resid 125 through 147 removed outlier: 5.148A pdb=" N VAL W 140 " --> pdb=" O LYS W 161 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS W 161 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU W 142 " --> pdb=" O THR W 159 " (cutoff:3.500A) removed outlier: 3.831A 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 Processing sheet with id=AC5, first strand: chain 'W' and resid 330 through 331 Processing sheet with id=AC6, first strand: chain 'X' and resid 44 through 45 removed outlier: 3.934A pdb=" N GLU X 45 " --> pdb=" O PHE X 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'X' and resid 102 through 106 removed outlier: 6.361A pdb=" N CYS X 103 " --> pdb=" O PHE X 309 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ASP X 311 " --> pdb=" O CYS X 103 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU X 105 " --> pdb=" O ASP X 311 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU X 308 " --> pdb=" O VAL X 337 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ALA X 339 " --> pdb=" O LEU X 308 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE X 310 " --> pdb=" O ALA X 339 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE X 75 " --> pdb=" O LEU X 338 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N SER X 340 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU X 77 " --> pdb=" O SER X 340 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 129 through 151 removed outlier: 6.408A pdb=" N GLY X 169 " --> pdb=" O THR X 145 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU X 147 " --> pdb=" O ILE X 167 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE X 167 " --> pdb=" O LEU X 147 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N HIS X 165 " --> pdb=" O PRO X 149 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP X 151 " --> pdb=" O ILE X 163 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE X 163 " --> pdb=" O ASP X 151 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL X 166 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY X 175 " --> pdb=" O SER X 172 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 175 through 181 current: chain 'X' and resid 210 through 215 removed outlier: 6.254A pdb=" N VAL X 230 " --> pdb=" O VAL X 212 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ARG X 214 " --> pdb=" O VAL X 230 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 344 through 346 Processing sheet with id=AD1, first strand: chain 'X' and resid 394 through 395 removed outlier: 7.236A pdb=" N GLN X 394 " --> pdb=" O ILE X 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'Y' and resid 40 through 41 removed outlier: 3.514A pdb=" N SER Y 41 " --> pdb=" O MET Y 44 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Y' and resid 98 through 102 removed outlier: 6.265A pdb=" N THR Y 99 " --> pdb=" O PHE Y 294 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP Y 296 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE Y 101 " --> pdb=" O ASP Y 296 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU Y 293 " --> pdb=" O MET Y 322 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ALA Y 324 " --> pdb=" O LEU Y 293 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE Y 295 " --> pdb=" O ALA Y 324 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ALA Y 70 " --> pdb=" O ILE Y 352 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Y' and resid 125 through 147 removed outlier: 5.273A pdb=" N VAL Y 140 " --> pdb=" O LYS Y 161 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS Y 161 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU Y 142 " --> pdb=" O THR Y 159 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY Y 156 " --> pdb=" O LEU Y 171 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU Y 171 " --> pdb=" O GLY Y 156 " (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: 5.462A pdb=" N VAL Y 222 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ARG Y 204 " --> pdb=" O VAL Y 222 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Y' and resid 329 through 331 Processing sheet with id=AD6, first strand: chain 'Q' and resid 949 through 954 removed outlier: 6.275A pdb=" N LEU Q1319 " --> pdb=" O ILE Q1390 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 1026 through 1027 removed outlier: 6.130A pdb=" N PHE Q1026 " --> pdb=" O SER Q1215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'Q' and resid 1082 through 1084 removed outlier: 6.178A pdb=" N TYR Q1083 " --> pdb=" O GLU Q1222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 1072 hydrogen bonds defined for protein. 3135 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: 9.63 Time building geometry restraints manager: 7.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9541 1.34 - 1.46: 5841 1.46 - 1.59: 13536 1.59 - 1.71: 18 1.71 - 1.83: 166 Bond restraints: 29102 Sorted by residual: bond pdb=" N TYR Y 212 " pdb=" CA TYR Y 212 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.28e-02 6.10e+03 9.33e+00 bond pdb=" N LEU X 224 " pdb=" CA LEU X 224 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.24e+00 bond pdb=" N GLU X 225 " pdb=" CA GLU X 225 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.23e-02 6.61e+03 8.11e+00 bond pdb=" N LEU Q1383 " pdb=" CA LEU Q1383 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.23e-02 6.61e+03 7.52e+00 bond pdb=" N VAL X 230 " pdb=" CA VAL X 230 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.23e-02 6.61e+03 5.93e+00 ... (remaining 29097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 39070 4.05 - 8.11: 252 8.11 - 12.16: 37 12.16 - 16.22: 10 16.22 - 20.27: 4 Bond angle restraints: 39373 Sorted by residual: angle pdb=" N ALA Q1386 " pdb=" CA ALA Q1386 " pdb=" C ALA Q1386 " ideal model delta sigma weight residual 108.32 88.05 20.27 1.64e+00 3.72e-01 1.53e+02 angle pdb=" N ALA Q1385 " pdb=" CA ALA Q1385 " pdb=" C ALA Q1385 " ideal model delta sigma weight residual 108.63 89.86 18.77 1.60e+00 3.91e-01 1.38e+02 angle pdb=" N ALA Q1386 " pdb=" CA ALA Q1386 " pdb=" CB ALA Q1386 " ideal model delta sigma weight residual 110.57 128.70 -18.13 1.69e+00 3.50e-01 1.15e+02 angle pdb=" N TYR T 462 " pdb=" CA TYR T 462 " pdb=" C TYR T 462 " ideal model delta sigma weight residual 111.39 124.25 -12.86 1.38e+00 5.25e-01 8.69e+01 angle pdb=" CA MET R 714 " pdb=" CB MET R 714 " pdb=" CG MET R 714 " ideal model delta sigma weight residual 114.10 125.57 -11.47 2.00e+00 2.50e-01 3.29e+01 ... (remaining 39368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 17190 35.78 - 71.56: 636 71.56 - 107.33: 47 107.33 - 143.11: 3 143.11 - 178.89: 4 Dihedral angle restraints: 17880 sinusoidal: 7318 harmonic: 10562 Sorted by residual: 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 -60.00 118.89 -178.89 1 2.00e+01 2.50e-03 4.80e+01 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 300.00 137.99 162.01 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP T 501 " pdb=" O3A ADP T 501 " pdb=" PA ADP T 501 " pdb=" PB ADP T 501 " ideal model delta sinusoidal sigma weight residual -60.00 93.12 -153.12 1 2.00e+01 2.50e-03 4.54e+01 ... (remaining 17877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 4478 0.117 - 0.234: 138 0.234 - 0.351: 2 0.351 - 0.469: 0 0.469 - 0.586: 2 Chirality restraints: 4620 Sorted by residual: chirality pdb=" CA ALA Q1385 " pdb=" N ALA Q1385 " pdb=" C ALA Q1385 " pdb=" CB ALA Q1385 " both_signs ideal model delta sigma weight residual False 2.48 3.07 -0.59 2.00e-01 2.50e+01 8.58e+00 chirality pdb=" CA TYR T 462 " pdb=" N TYR T 462 " pdb=" C TYR T 462 " pdb=" CB TYR T 462 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.99e+00 chirality pdb=" CB VAL Q1152 " pdb=" CA VAL Q1152 " pdb=" CG1 VAL Q1152 " pdb=" CG2 VAL Q1152 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 4617 not shown) Planarity restraints: 5040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE X 222 " 0.025 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C PHE X 222 " -0.087 2.00e-02 2.50e+03 pdb=" O PHE X 222 " 0.033 2.00e-02 2.50e+03 pdb=" N ASP X 223 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA S 148 " -0.069 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO S 149 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO S 149 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO S 149 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP S 69 " -0.015 2.00e-02 2.50e+03 3.13e-02 9.77e+00 pdb=" CG ASP S 69 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASP S 69 " -0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP S 69 " -0.019 2.00e-02 2.50e+03 ... (remaining 5037 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 30 2.37 - 3.00: 13641 3.00 - 3.63: 42069 3.63 - 4.27: 63347 4.27 - 4.90: 107873 Nonbonded interactions: 226960 Sorted by model distance: nonbonded pdb=" CH2 TRP Q1361 " pdb=" O ALA Q1385 " model vdw 1.735 3.340 nonbonded pdb=" O ARG V 413 " pdb=" OE1 GLN V 417 " model vdw 1.834 3.040 nonbonded pdb=" CZ2 TRP Q1361 " pdb=" O ALA Q1385 " model vdw 1.856 3.340 nonbonded pdb=" CD1 ILE W 303 " pdb=" CG2 THR W 335 " model vdw 2.152 3.880 nonbonded pdb=" OG SER Y 24 " pdb=" OE2 GLU Y 374 " model vdw 2.220 3.040 ... (remaining 226955 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'T' and (resid 22 through 463 or resid 501)) selection = (chain 'V' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 463 or resid 501)) selection = (chain 'X' and (resid 22 through 152 or (resid 161 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 463 or resid 501)) } ncs_group { reference = (chain 'U' and (resid 18 through 459 or resid 501)) selection = (chain 'W' and (resid 18 through 210 or resid 221 through 459 or resid 501)) selection = (chain 'Y' and (resid 18 through 210 or resid 221 through 459 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.230 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: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 60.030 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.110 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: 0.020 Load rotamer database and sin/cos tables:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.150 29104 Z= 0.240 Angle : 0.921 20.273 39373 Z= 0.481 Chirality : 0.052 0.586 4620 Planarity : 0.006 0.105 5040 Dihedral : 17.824 178.892 11060 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.06 % Allowed : 26.13 % Favored : 73.81 % 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: -1.69 (0.12), residues: 3618 helix: -1.44 (0.11), residues: 1475 sheet: 0.58 (0.20), residues: 672 loop : -1.46 (0.15), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Q1361 HIS 0.022 0.001 HIS U 153 PHE 0.035 0.002 PHE S 32 TYR 0.022 0.002 TYR V 462 ARG 0.010 0.001 ARG Q1431 Details of bonding type rmsd hydrogen bonds : bond 0.17152 ( 1072) hydrogen bonds : angle 6.36809 ( 3135) covalent geometry : bond 0.00491 (29102) covalent geometry : angle 0.92095 (39373) Misc. bond : bond 0.10629 ( 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 943 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 941 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.7596 (p0) cc_final: 0.7272 (p0) REVERT: R 38 SER cc_start: 0.7797 (t) cc_final: 0.7530 (m) REVERT: R 69 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7756 (mtpt) REVERT: R 95 GLN cc_start: 0.8166 (mt0) cc_final: 0.7698 (mt0) REVERT: R 97 ARG cc_start: 0.7509 (ttp-110) cc_final: 0.7060 (ttp-110) REVERT: R 112 GLU cc_start: 0.6960 (tt0) cc_final: 0.6651 (tt0) REVERT: R 121 HIS cc_start: 0.8310 (m-70) cc_final: 0.7971 (m-70) REVERT: R 144 GLN cc_start: 0.7226 (pm20) cc_final: 0.6393 (pm20) REVERT: R 193 ASP cc_start: 0.7376 (p0) cc_final: 0.7047 (p0) REVERT: R 249 ASP cc_start: 0.7708 (m-30) cc_final: 0.7171 (m-30) REVERT: R 262 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7421 (mm-30) REVERT: R 275 VAL cc_start: 0.7843 (t) cc_final: 0.7419 (m) REVERT: R 277 VAL cc_start: 0.7507 (m) cc_final: 0.7059 (p) REVERT: R 601 HIS cc_start: 0.7000 (t70) cc_final: 0.6643 (t70) REVERT: R 608 GLU cc_start: 0.7167 (tt0) cc_final: 0.6640 (tt0) REVERT: R 609 GLN cc_start: 0.7814 (mt0) cc_final: 0.7487 (mt0) REVERT: R 615 ASN cc_start: 0.8366 (p0) cc_final: 0.8114 (p0) REVERT: R 623 GLU cc_start: 0.8082 (tp30) cc_final: 0.7669 (tm-30) REVERT: R 659 GLN cc_start: 0.6976 (mm-40) cc_final: 0.6684 (mm-40) REVERT: R 681 LYS cc_start: 0.8023 (ttpt) cc_final: 0.7802 (ttpp) REVERT: R 697 ASN cc_start: 0.8146 (m-40) cc_final: 0.7879 (m110) REVERT: R 705 ASP cc_start: 0.7315 (t0) cc_final: 0.7071 (t0) REVERT: R 733 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7104 (mp0) REVERT: R 743 LYS cc_start: 0.7466 (tptm) cc_final: 0.7071 (tttp) REVERT: R 744 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7985 (mt-10) REVERT: R 751 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7479 (ttpt) REVERT: T 31 LYS cc_start: 0.8391 (mmtp) cc_final: 0.7966 (mmtt) REVERT: T 37 GLU cc_start: 0.7134 (pm20) cc_final: 0.6854 (pm20) REVERT: T 141 GLU cc_start: 0.7945 (tp30) cc_final: 0.7598 (mm-30) REVERT: T 146 GLU cc_start: 0.7935 (tt0) cc_final: 0.7654 (tt0) REVERT: T 167 ILE cc_start: 0.8145 (mp) cc_final: 0.7822 (mp) REVERT: T 180 ARG cc_start: 0.7778 (mtp-110) cc_final: 0.7416 (mtt-85) REVERT: T 187 GLU cc_start: 0.6708 (tp30) cc_final: 0.6305 (tp30) REVERT: T 205 ASN cc_start: 0.7524 (m-40) cc_final: 0.7168 (m-40) REVERT: T 206 THR cc_start: 0.7644 (m) cc_final: 0.6644 (p) REVERT: T 227 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7292 (mt-10) REVERT: T 234 LYS cc_start: 0.8407 (mmmm) cc_final: 0.7927 (mmmm) REVERT: T 269 MET cc_start: 0.6760 (mmm) cc_final: 0.6380 (mmm) REVERT: T 279 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7624 (mt-10) REVERT: T 282 GLU cc_start: 0.7331 (pm20) cc_final: 0.7054 (pm20) REVERT: T 294 LYS cc_start: 0.7952 (ttmm) cc_final: 0.7693 (ttpt) REVERT: T 312 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7880 (mp0) REVERT: T 345 THR cc_start: 0.8298 (m) cc_final: 0.7845 (p) REVERT: T 386 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7449 (mpt180) REVERT: T 392 ARG cc_start: 0.7594 (mtm110) cc_final: 0.6974 (mtm-85) REVERT: T 393 LEU cc_start: 0.7659 (mt) cc_final: 0.7437 (mt) REVERT: T 429 SER cc_start: 0.8061 (t) cc_final: 0.7846 (m) REVERT: T 432 LYS cc_start: 0.8228 (pmtt) cc_final: 0.7938 (pmtt) REVERT: T 441 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7285 (tt0) REVERT: T 454 LYS cc_start: 0.7703 (tttt) cc_final: 0.7496 (ttmm) REVERT: U 32 ASP cc_start: 0.7544 (m-30) cc_final: 0.7202 (m-30) REVERT: U 36 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7293 (mm110) REVERT: U 65 THR cc_start: 0.7995 (p) cc_final: 0.7763 (t) REVERT: U 90 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7649 (mm-40) REVERT: U 105 GLU cc_start: 0.7776 (tt0) cc_final: 0.7434 (mt-10) REVERT: U 110 GLU cc_start: 0.7604 (pp20) cc_final: 0.7175 (pp20) REVERT: U 142 GLU cc_start: 0.7679 (tt0) cc_final: 0.7061 (tm-30) REVERT: U 164 ASP cc_start: 0.8116 (m-30) cc_final: 0.7896 (m-30) REVERT: U 170 GLU cc_start: 0.7766 (tt0) cc_final: 0.7482 (tp30) REVERT: U 174 LYS cc_start: 0.7599 (mtpt) cc_final: 0.7382 (mtpt) REVERT: U 282 GLU cc_start: 0.7706 (tp30) cc_final: 0.7494 (tp30) REVERT: U 285 LYS cc_start: 0.8176 (mttp) cc_final: 0.7863 (mttm) REVERT: U 296 ASP cc_start: 0.8144 (t0) cc_final: 0.7858 (t70) REVERT: U 297 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7958 (mp0) REVERT: U 323 MET cc_start: 0.8781 (mtm) cc_final: 0.8563 (mtp) REVERT: U 327 ARG cc_start: 0.8064 (mmm160) cc_final: 0.7842 (mmm160) REVERT: U 373 GLN cc_start: 0.7649 (mt0) cc_final: 0.7371 (mt0) REVERT: U 374 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7147 (mm-30) REVERT: U 376 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6891 (mm-30) REVERT: U 393 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6961 (tp30) REVERT: U 395 SER cc_start: 0.8113 (t) cc_final: 0.7402 (p) REVERT: U 407 GLN cc_start: 0.8000 (tt0) cc_final: 0.7698 (tp40) REVERT: U 438 LYS cc_start: 0.7904 (ttpp) cc_final: 0.7628 (ttmm) REVERT: U 451 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7661 (mp-120) REVERT: V 23 ARG cc_start: 0.7809 (ttp80) cc_final: 0.7437 (ttt-90) REVERT: V 36 ASP cc_start: 0.7455 (m-30) cc_final: 0.7148 (m-30) REVERT: V 42 LYS cc_start: 0.7806 (mtmm) cc_final: 0.7231 (tttm) REVERT: V 148 THR cc_start: 0.8154 (m) cc_final: 0.7617 (p) REVERT: V 154 ASN cc_start: 0.7338 (t0) cc_final: 0.6911 (t0) REVERT: V 177 LYS cc_start: 0.8471 (ttmt) cc_final: 0.8114 (tttm) REVERT: V 190 GLN cc_start: 0.7981 (tt0) cc_final: 0.7651 (tt0) REVERT: V 214 ARG cc_start: 0.7667 (mmt180) cc_final: 0.7250 (mmt180) REVERT: V 216 ASP cc_start: 0.7066 (p0) cc_final: 0.6673 (p0) REVERT: V 221 GLU cc_start: 0.7030 (pm20) cc_final: 0.6819 (tm-30) REVERT: V 227 GLU cc_start: 0.7764 (tt0) cc_final: 0.7535 (mt-10) REVERT: V 236 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7859 (mt-10) REVERT: V 287 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7581 (mm-30) REVERT: V 294 LYS cc_start: 0.7694 (ttpp) cc_final: 0.7463 (ttpp) REVERT: V 298 GLN cc_start: 0.7684 (mp10) cc_final: 0.7153 (mp10) REVERT: V 376 ASP cc_start: 0.6983 (m-30) cc_final: 0.6738 (m-30) REVERT: V 385 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7059 (mm-30) REVERT: V 394 GLN cc_start: 0.7919 (pt0) cc_final: 0.7527 (pt0) REVERT: V 427 GLN cc_start: 0.7750 (tp40) cc_final: 0.7498 (tp40) REVERT: V 432 LYS cc_start: 0.7483 (mttt) cc_final: 0.7061 (tppt) REVERT: W 36 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7353 (mm-40) REVERT: W 107 PHE cc_start: 0.8566 (m-80) cc_final: 0.8308 (m-80) REVERT: W 130 LYS cc_start: 0.7992 (ttmm) cc_final: 0.7549 (ttpp) REVERT: W 170 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7737 (mt-10) REVERT: W 181 LYS cc_start: 0.7837 (ttpp) cc_final: 0.7277 (ttmt) REVERT: W 182 GLU cc_start: 0.7488 (tp30) cc_final: 0.6807 (pp20) REVERT: W 188 ASP cc_start: 0.7429 (m-30) cc_final: 0.7159 (m-30) REVERT: W 198 LYS cc_start: 0.8344 (tttt) cc_final: 0.8118 (tttt) REVERT: W 252 GLN cc_start: 0.7932 (mt0) cc_final: 0.7622 (tp40) REVERT: W 261 ASP cc_start: 0.8120 (t0) cc_final: 0.7891 (t70) REVERT: W 285 LYS cc_start: 0.8088 (ttmm) cc_final: 0.7842 (ttpp) REVERT: W 300 MET cc_start: 0.8172 (mmm) cc_final: 0.7959 (mmm) REVERT: W 374 GLU cc_start: 0.7192 (tp30) cc_final: 0.6725 (tp30) REVERT: W 378 GLU cc_start: 0.7625 (mp0) cc_final: 0.7179 (mm-30) REVERT: W 381 SER cc_start: 0.7033 (m) cc_final: 0.6778 (p) REVERT: W 385 ASP cc_start: 0.7369 (m-30) cc_final: 0.6910 (m-30) REVERT: W 422 ASP cc_start: 0.8142 (m-30) cc_final: 0.7895 (m-30) REVERT: W 425 ARG cc_start: 0.7618 (ttt90) cc_final: 0.7295 (ttt180) REVERT: W 433 SER cc_start: 0.7133 (t) cc_final: 0.6837 (m) REVERT: W 438 LYS cc_start: 0.7544 (ttmt) cc_final: 0.7286 (ttmm) REVERT: W 444 GLU cc_start: 0.7275 (mt-10) cc_final: 0.7070 (mt-10) REVERT: W 449 ASP cc_start: 0.7382 (t70) cc_final: 0.7004 (t70) REVERT: W 451 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7492 (mm-40) REVERT: W 455 GLN cc_start: 0.7404 (mm110) cc_final: 0.7057 (tt0) REVERT: X 37 GLU cc_start: 0.7582 (pp20) cc_final: 0.7279 (pp20) REVERT: X 63 ASP cc_start: 0.8001 (m-30) cc_final: 0.7759 (m-30) REVERT: X 125 PHE cc_start: 0.7797 (t80) cc_final: 0.7576 (t80) REVERT: X 134 LYS cc_start: 0.7800 (ptpt) cc_final: 0.7495 (ptpp) REVERT: X 138 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7522 (mm-30) REVERT: X 140 TYR cc_start: 0.7857 (m-80) cc_final: 0.7466 (m-80) REVERT: X 150 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6954 (tt0) REVERT: X 156 LEU cc_start: 0.8650 (mt) cc_final: 0.8356 (mp) REVERT: X 177 LYS cc_start: 0.8101 (ttmt) cc_final: 0.7744 (ttmm) REVERT: X 182 ASP cc_start: 0.8247 (t70) cc_final: 0.7714 (t0) REVERT: X 192 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7529 (mm-30) REVERT: X 196 ILE cc_start: 0.8202 (mt) cc_final: 0.7903 (mp) REVERT: X 218 TYR cc_start: 0.8076 (m-80) cc_final: 0.7560 (m-80) REVERT: X 221 GLU cc_start: 0.7551 (tp30) cc_final: 0.7154 (tt0) REVERT: X 229 TYR cc_start: 0.7400 (m-80) cc_final: 0.6603 (m-80) REVERT: X 232 LEU cc_start: 0.8702 (tt) cc_final: 0.8438 (tm) REVERT: X 242 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7474 (mp0) REVERT: X 243 ILE cc_start: 0.7588 (mt) cc_final: 0.7364 (mm) REVERT: X 282 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6777 (tm-30) REVERT: X 286 GLN cc_start: 0.7611 (mm110) cc_final: 0.7269 (mm110) REVERT: X 295 TYR cc_start: 0.7661 (m-80) cc_final: 0.7454 (m-80) REVERT: X 302 GLU cc_start: 0.7767 (tp30) cc_final: 0.7435 (tp30) REVERT: X 317 ASP cc_start: 0.7183 (t0) cc_final: 0.6894 (m-30) REVERT: X 341 ASN cc_start: 0.8301 (p0) cc_final: 0.7936 (p0) REVERT: X 351 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6968 (mm-30) REVERT: X 390 VAL cc_start: 0.7487 (t) cc_final: 0.7277 (p) REVERT: X 429 SER cc_start: 0.7911 (t) cc_final: 0.7443 (p) REVERT: Y 59 LYS cc_start: 0.7916 (tppt) cc_final: 0.7499 (tppp) REVERT: Y 69 ARG cc_start: 0.7916 (mtt90) cc_final: 0.7470 (mmm-85) REVERT: Y 110 GLU cc_start: 0.7617 (pt0) cc_final: 0.7394 (pt0) REVERT: Y 130 LYS cc_start: 0.8198 (ttmm) cc_final: 0.7980 (ttpp) REVERT: Y 165 MET cc_start: 0.8321 (ptp) cc_final: 0.7749 (ppp) REVERT: Y 202 LEU cc_start: 0.8338 (mm) cc_final: 0.8089 (mp) REVERT: Y 226 GLU cc_start: 0.7367 (mp0) cc_final: 0.7041 (mp0) REVERT: Y 233 LYS cc_start: 0.7385 (ttmt) cc_final: 0.7130 (ttpp) REVERT: Y 236 VAL cc_start: 0.8344 (m) cc_final: 0.8121 (t) REVERT: Y 266 ARG cc_start: 0.7555 (mtm110) cc_final: 0.7291 (mtm110) REVERT: Y 282 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7573 (tm-30) REVERT: Y 287 GLU cc_start: 0.7688 (pt0) cc_final: 0.7117 (pm20) REVERT: Y 297 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8082 (mm-30) REVERT: Y 317 PHE cc_start: 0.8413 (m-80) cc_final: 0.8064 (m-80) REVERT: Y 327 ARG cc_start: 0.8329 (mmt-90) cc_final: 0.8073 (mmt-90) REVERT: Y 331 LYS cc_start: 0.8050 (ttpt) cc_final: 0.7778 (ttpt) REVERT: Y 350 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.7222 (mtm-85) REVERT: Y 357 LYS cc_start: 0.8230 (mttm) cc_final: 0.7766 (mmmm) REVERT: Y 374 GLU cc_start: 0.6621 (tt0) cc_final: 0.6245 (tt0) REVERT: Y 376 GLU cc_start: 0.7686 (mp0) cc_final: 0.7426 (mm-30) REVERT: Y 378 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7092 (pm20) REVERT: Y 381 SER cc_start: 0.7115 (m) cc_final: 0.6820 (t) REVERT: Y 417 THR cc_start: 0.7822 (p) cc_final: 0.7396 (t) REVERT: Y 422 ASP cc_start: 0.8098 (m-30) cc_final: 0.7749 (m-30) REVERT: Y 439 TYR cc_start: 0.7861 (m-80) cc_final: 0.7233 (m-80) REVERT: Y 444 GLU cc_start: 0.7925 (tt0) cc_final: 0.7347 (tp30) REVERT: Q 1072 ASP cc_start: 0.8038 (m-30) cc_final: 0.7779 (m-30) REVERT: Q 1078 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7381 (mtm-85) REVERT: Q 1083 TYR cc_start: 0.8208 (t80) cc_final: 0.7963 (t80) REVERT: Q 1103 ASP cc_start: 0.7689 (p0) cc_final: 0.6362 (p0) REVERT: Q 1106 ASN cc_start: 0.7906 (t0) cc_final: 0.7667 (t0) REVERT: Q 1123 GLU cc_start: 0.7691 (mp0) cc_final: 0.7449 (mp0) REVERT: Q 1134 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7408 (mm-30) REVERT: Q 1146 THR cc_start: 0.7240 (p) cc_final: 0.5854 (m) REVERT: Q 1226 SER cc_start: 0.8269 (t) cc_final: 0.8048 (t) REVERT: Q 1231 ASN cc_start: 0.7794 (m-40) cc_final: 0.7438 (m-40) REVERT: Q 1239 ASP cc_start: 0.7131 (t0) cc_final: 0.6808 (t70) REVERT: Q 1260 LYS cc_start: 0.8475 (mtpp) cc_final: 0.8089 (mtpp) REVERT: Q 1266 GLU cc_start: 0.7651 (mp0) cc_final: 0.7042 (mp0) REVERT: Q 1280 LYS cc_start: 0.8046 (ptpp) cc_final: 0.7729 (ptpp) REVERT: Q 1301 LEU cc_start: 0.7155 (tp) cc_final: 0.6910 (tt) REVERT: Q 1305 ASP cc_start: 0.7705 (m-30) cc_final: 0.7295 (m-30) outliers start: 2 outliers final: 1 residues processed: 941 average time/residue: 1.5796 time to fit residues: 1697.2435 Evaluate side-chains 818 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 817 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 196 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 146 optimal weight: 0.1980 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 327 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 121 HIS ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 GLN R 633 GLN S 162 ASN T 29 HIS U 144 GLN U 237 HIS U 272 GLN U 441 GLN U 446 GLN U 455 GLN V 51 GLN V 263 GLN V 331 ASN V 417 GLN W 144 GLN W 155 GLN W 173 ASN X 271 GLN X 325 ASN Y 248 ASN Y 272 GLN Y 310 ASN Q1211 HIS Q1244 GLN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1316 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.119741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.099056 restraints weight = 44295.478| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.15 r_work: 0.3188 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 29104 Z= 0.232 Angle : 0.664 7.764 39373 Z= 0.332 Chirality : 0.047 0.177 4620 Planarity : 0.005 0.071 5040 Dihedral : 7.787 139.394 4006 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.70 % Allowed : 24.58 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.55 (0.13), residues: 3618 helix: 0.06 (0.13), residues: 1509 sheet: 0.53 (0.19), residues: 669 loop : -1.17 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Q1396 HIS 0.005 0.001 HIS T 250 PHE 0.030 0.002 PHE R 691 TYR 0.028 0.002 TYR V 462 ARG 0.009 0.001 ARG V 371 Details of bonding type rmsd hydrogen bonds : bond 0.05339 ( 1072) hydrogen bonds : angle 4.35869 ( 3135) covalent geometry : bond 0.00553 (29102) covalent geometry : angle 0.66382 (39373) Misc. bond : bond 0.00843 ( 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 974 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 857 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.8557 (p0) cc_final: 0.8133 (p0) REVERT: R 38 SER cc_start: 0.8528 (t) cc_final: 0.8306 (m) REVERT: R 70 PHE cc_start: 0.7818 (t80) cc_final: 0.7576 (t80) REVERT: R 95 GLN cc_start: 0.8368 (mt0) cc_final: 0.8134 (mt0) REVERT: R 112 GLU cc_start: 0.7854 (tt0) cc_final: 0.7545 (tt0) REVERT: R 193 ASP cc_start: 0.7769 (p0) cc_final: 0.7566 (p0) REVERT: R 238 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7933 (mtm) REVERT: R 246 MET cc_start: 0.8659 (ptt) cc_final: 0.8365 (ptp) REVERT: R 249 ASP cc_start: 0.8179 (m-30) cc_final: 0.7905 (m-30) REVERT: R 266 THR cc_start: 0.8017 (m) cc_final: 0.7601 (p) REVERT: R 608 GLU cc_start: 0.8369 (tt0) cc_final: 0.7894 (tt0) REVERT: R 617 GLU cc_start: 0.8302 (mp0) cc_final: 0.8004 (mp0) REVERT: R 623 GLU cc_start: 0.8624 (tp30) cc_final: 0.8252 (tm-30) REVERT: R 643 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8103 (tm-30) REVERT: R 648 LYS cc_start: 0.8759 (mtpp) cc_final: 0.8484 (mtpp) REVERT: R 659 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7925 (mm-40) REVERT: R 681 LYS cc_start: 0.8776 (ttpt) cc_final: 0.8569 (ttpp) REVERT: R 682 GLU cc_start: 0.8720 (mp0) cc_final: 0.8325 (mp0) REVERT: R 697 ASN cc_start: 0.8365 (m-40) cc_final: 0.8163 (m110) REVERT: R 751 LYS cc_start: 0.8566 (ttpt) cc_final: 0.8172 (ttpt) REVERT: S 77 LEU cc_start: 0.8756 (mp) cc_final: 0.8551 (mt) REVERT: S 80 LYS cc_start: 0.8697 (tmmt) cc_final: 0.8437 (tmmt) REVERT: T 37 GLU cc_start: 0.7372 (pm20) cc_final: 0.7106 (pm20) REVERT: T 90 LEU cc_start: 0.8799 (mm) cc_final: 0.8587 (mt) REVERT: T 187 GLU cc_start: 0.7646 (tp30) cc_final: 0.7138 (tp30) REVERT: T 203 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: T 205 ASN cc_start: 0.8487 (m-40) cc_final: 0.8014 (m-40) REVERT: T 206 THR cc_start: 0.8750 (m) cc_final: 0.8153 (p) REVERT: T 234 LYS cc_start: 0.8567 (mmmm) cc_final: 0.8312 (mmmm) REVERT: T 279 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7792 (mt-10) REVERT: T 285 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8616 (mtt90) REVERT: T 386 ARG cc_start: 0.8718 (ttm-80) cc_final: 0.8388 (mpt180) REVERT: T 392 ARG cc_start: 0.8313 (mtm110) cc_final: 0.7953 (mtm-85) REVERT: U 32 ASP cc_start: 0.7937 (m-30) cc_final: 0.7714 (m-30) REVERT: U 36 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8103 (mm110) REVERT: U 71 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8453 (p) REVERT: U 110 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7588 (pp20) REVERT: U 174 LYS cc_start: 0.8068 (mtpt) cc_final: 0.7859 (mtpt) REVERT: U 200 THR cc_start: 0.8961 (p) cc_final: 0.8746 (t) REVERT: U 255 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8643 (mp) REVERT: U 271 ASP cc_start: 0.8121 (m-30) cc_final: 0.7868 (m-30) REVERT: V 36 ASP cc_start: 0.7717 (m-30) cc_final: 0.7221 (m-30) REVERT: V 42 LYS cc_start: 0.8283 (mtmm) cc_final: 0.7970 (tttm) REVERT: V 135 GLU cc_start: 0.7513 (tt0) cc_final: 0.7283 (tt0) REVERT: V 148 THR cc_start: 0.8754 (m) cc_final: 0.8504 (p) REVERT: V 154 ASN cc_start: 0.7954 (t0) cc_final: 0.7614 (t0) REVERT: V 161 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8503 (ttmm) REVERT: V 198 ASP cc_start: 0.8068 (m-30) cc_final: 0.7561 (m-30) REVERT: V 203 GLU cc_start: 0.8028 (tt0) cc_final: 0.7757 (tt0) REVERT: V 268 MET cc_start: 0.8510 (mmm) cc_final: 0.8208 (mmm) REVERT: V 294 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7966 (ttpp) REVERT: V 298 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: W 130 LYS cc_start: 0.8476 (ttmm) cc_final: 0.8253 (ttpp) REVERT: W 177 ASP cc_start: 0.8579 (m-30) cc_final: 0.8355 (m-30) REVERT: W 182 GLU cc_start: 0.7774 (tp30) cc_final: 0.7416 (tm-30) REVERT: W 283 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7533 (tm-30) REVERT: W 338 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8657 (mttm) REVERT: W 374 GLU cc_start: 0.7786 (tp30) cc_final: 0.7476 (tp30) REVERT: W 385 ASP cc_start: 0.8171 (m-30) cc_final: 0.7856 (m-30) REVERT: W 405 VAL cc_start: 0.8137 (t) cc_final: 0.7894 (m) REVERT: W 421 GLU cc_start: 0.8276 (mp0) cc_final: 0.7988 (mp0) REVERT: W 422 ASP cc_start: 0.8672 (m-30) cc_final: 0.8470 (m-30) REVERT: W 425 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8343 (ttt90) REVERT: X 37 GLU cc_start: 0.7744 (pp20) cc_final: 0.7489 (pp20) REVERT: X 94 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7855 (mt0) REVERT: X 125 PHE cc_start: 0.8856 (t80) cc_final: 0.8644 (t80) REVERT: X 140 TYR cc_start: 0.8884 (m-80) cc_final: 0.8657 (m-80) REVERT: X 192 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7725 (mm-30) REVERT: X 203 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6569 (tm-30) REVERT: X 282 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7913 (tm-30) REVERT: X 341 ASN cc_start: 0.8856 (p0) cc_final: 0.8562 (p0) REVERT: Y 144 GLN cc_start: 0.7128 (mp10) cc_final: 0.6883 (mp10) REVERT: Y 184 VAL cc_start: 0.9133 (m) cc_final: 0.8890 (t) REVERT: Y 202 LEU cc_start: 0.8899 (mm) cc_final: 0.8598 (mp) REVERT: Y 261 ASP cc_start: 0.8097 (p0) cc_final: 0.7886 (p0) REVERT: Y 282 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8117 (tm-30) REVERT: Y 350 ARG cc_start: 0.8295 (mtm-85) cc_final: 0.8017 (mtp85) REVERT: Y 357 LYS cc_start: 0.8749 (mttm) cc_final: 0.8479 (mtmm) REVERT: Q 957 THR cc_start: 0.7674 (p) cc_final: 0.7281 (t) REVERT: Q 1021 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: Q 1103 ASP cc_start: 0.8733 (p0) cc_final: 0.7526 (p0) REVERT: Q 1146 THR cc_start: 0.8635 (p) cc_final: 0.8245 (p) REVERT: Q 1160 LYS cc_start: 0.7931 (ptpp) cc_final: 0.7641 (ptpp) REVERT: Q 1266 GLU cc_start: 0.7945 (mp0) cc_final: 0.7512 (mp0) REVERT: Q 1280 LYS cc_start: 0.8604 (ptpp) cc_final: 0.8390 (ptpp) REVERT: Q 1301 LEU cc_start: 0.8470 (tp) cc_final: 0.8109 (tt) REVERT: Q 1305 ASP cc_start: 0.8288 (m-30) cc_final: 0.7978 (m-30) REVERT: Q 1432 MET cc_start: 0.6283 (tpp) cc_final: 0.6019 (tpp) REVERT: Z 314 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7962 (pp20) outliers start: 117 outliers final: 44 residues processed: 910 average time/residue: 1.6393 time to fit residues: 1705.1940 Evaluate side-chains 864 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 807 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 145 SER Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain T residue 285 ARG Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain T residue 398 SER Chi-restraints excluded: chain U residue 60 MET Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 411 MET Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 161 LYS Chi-restraints excluded: chain V residue 298 GLN Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 325 ASN Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain W residue 160 ILE Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 233 LYS Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 338 LYS Chi-restraints excluded: chain W residue 373 GLN Chi-restraints excluded: chain W residue 425 ARG Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 243 ILE Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 163 THR Chi-restraints excluded: chain Y residue 188 ASP Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 238 THR Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 323 MET Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 374 GLU Chi-restraints excluded: chain Y residue 436 SER Chi-restraints excluded: chain Q residue 983 THR Chi-restraints excluded: chain Q residue 1021 ASP Chi-restraints excluded: chain Q residue 1150 LYS Chi-restraints excluded: chain Q residue 1161 ASN Chi-restraints excluded: chain Q residue 1203 LEU Chi-restraints excluded: chain Q residue 1233 ILE Chi-restraints excluded: chain Z residue 314 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 49 optimal weight: 5.9990 chunk 330 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 348 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 199 optimal weight: 0.5980 chunk 272 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 633 GLN R 749 ASN U 144 GLN U 237 HIS U 362 GLN U 407 GLN U 446 GLN U 455 GLN V 51 GLN V 263 GLN V 394 GLN V 417 GLN W 47 GLN W 173 ASN X 271 GLN X 289 ASN X 325 ASN Y 49 GLN Y 310 ASN Q1244 GLN Q1403 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.119768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.099328 restraints weight = 44268.333| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.24 r_work: 0.3198 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29104 Z= 0.168 Angle : 0.601 7.888 39373 Z= 0.299 Chirality : 0.044 0.162 4620 Planarity : 0.004 0.054 5040 Dihedral : 7.285 131.367 4004 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.11 % Allowed : 25.66 % Favored : 70.23 % 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: 0.68 (0.13), residues: 1515 sheet: 0.61 (0.19), residues: 675 loop : -1.07 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 108 HIS 0.005 0.001 HIS V 165 PHE 0.026 0.001 PHE R 691 TYR 0.022 0.002 TYR V 462 ARG 0.009 0.000 ARG V 431 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 1072) hydrogen bonds : angle 4.12217 ( 3135) covalent geometry : bond 0.00401 (29102) covalent geometry : angle 0.60115 (39373) Misc. bond : bond 0.00125 ( 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 944 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 814 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.8546 (p0) cc_final: 0.8114 (p0) REVERT: R 38 SER cc_start: 0.8533 (t) cc_final: 0.8280 (m) REVERT: R 70 PHE cc_start: 0.7785 (t80) cc_final: 0.7548 (t80) REVERT: R 74 LYS cc_start: 0.8333 (pptt) cc_final: 0.8120 (pptt) REVERT: R 95 GLN cc_start: 0.8507 (mt0) cc_final: 0.8201 (mt0) REVERT: R 112 GLU cc_start: 0.7865 (tt0) cc_final: 0.7430 (mt-10) REVERT: R 121 HIS cc_start: 0.8575 (OUTLIER) cc_final: 0.8169 (m-70) REVERT: R 193 ASP cc_start: 0.7738 (p0) cc_final: 0.7505 (p0) REVERT: R 238 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7747 (mtm) REVERT: R 241 LEU cc_start: 0.8808 (mp) cc_final: 0.8506 (mp) REVERT: R 242 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7423 (mt0) REVERT: R 244 GLU cc_start: 0.7933 (tt0) cc_final: 0.7633 (tm-30) REVERT: R 249 ASP cc_start: 0.8163 (m-30) cc_final: 0.7868 (m-30) REVERT: R 268 GLU cc_start: 0.7793 (pm20) cc_final: 0.7219 (pp20) REVERT: R 278 GLU cc_start: 0.7967 (tt0) cc_final: 0.7294 (tm-30) REVERT: R 617 GLU cc_start: 0.8263 (mp0) cc_final: 0.7959 (mp0) REVERT: R 643 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8033 (tp30) REVERT: R 659 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7925 (mm-40) REVERT: R 697 ASN cc_start: 0.8404 (m-40) cc_final: 0.8152 (m110) REVERT: R 751 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8164 (ttpt) REVERT: S 77 LEU cc_start: 0.8704 (mp) cc_final: 0.8475 (mt) REVERT: S 80 LYS cc_start: 0.8704 (tmmt) cc_final: 0.8457 (tmmt) REVERT: T 37 GLU cc_start: 0.7359 (pm20) cc_final: 0.7070 (pm20) REVERT: T 82 SER cc_start: 0.9003 (p) cc_final: 0.8760 (t) REVERT: T 90 LEU cc_start: 0.8750 (mm) cc_final: 0.8536 (mt) REVERT: T 203 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: T 205 ASN cc_start: 0.8451 (m-40) cc_final: 0.7917 (m-40) REVERT: T 206 THR cc_start: 0.8727 (m) cc_final: 0.8180 (p) REVERT: T 234 LYS cc_start: 0.8548 (mmmm) cc_final: 0.8273 (mmmm) REVERT: T 386 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8391 (mpt180) REVERT: T 392 ARG cc_start: 0.8243 (mtm110) cc_final: 0.7887 (mtm-85) REVERT: U 32 ASP cc_start: 0.7980 (m-30) cc_final: 0.7725 (m-30) REVERT: U 71 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8417 (p) REVERT: U 110 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7570 (pp20) REVERT: U 135 LEU cc_start: 0.8781 (mt) cc_final: 0.8510 (mm) REVERT: U 170 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7922 (tp30) REVERT: U 174 LYS cc_start: 0.8096 (mtpt) cc_final: 0.7883 (mtpt) REVERT: U 271 ASP cc_start: 0.8111 (m-30) cc_final: 0.7840 (m-30) REVERT: U 297 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: U 350 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.7798 (mtp85) REVERT: V 36 ASP cc_start: 0.7745 (m-30) cc_final: 0.7211 (m-30) REVERT: V 42 LYS cc_start: 0.8292 (mtmm) cc_final: 0.7890 (tttm) REVERT: V 135 GLU cc_start: 0.7536 (tt0) cc_final: 0.7293 (tt0) REVERT: V 148 THR cc_start: 0.8753 (m) cc_final: 0.8493 (p) REVERT: V 154 ASN cc_start: 0.8009 (t0) cc_final: 0.7667 (t0) REVERT: V 161 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8621 (ttmm) REVERT: V 203 GLU cc_start: 0.8086 (tt0) cc_final: 0.7791 (tt0) REVERT: W 130 LYS cc_start: 0.8464 (ttmm) cc_final: 0.8254 (ttpp) REVERT: W 177 ASP cc_start: 0.8584 (m-30) cc_final: 0.8325 (m-30) REVERT: W 204 ARG cc_start: 0.8252 (ttt90) cc_final: 0.7859 (ttt90) REVERT: W 283 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7400 (tm-30) REVERT: W 338 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8653 (mttm) REVERT: W 385 ASP cc_start: 0.8128 (m-30) cc_final: 0.7776 (m-30) REVERT: W 389 LYS cc_start: 0.8489 (mmmm) cc_final: 0.8066 (mmmm) REVERT: W 393 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7315 (mt-10) REVERT: W 405 VAL cc_start: 0.7975 (t) cc_final: 0.7745 (m) REVERT: W 413 ARG cc_start: 0.8565 (mtm180) cc_final: 0.8292 (mtm180) REVERT: W 421 GLU cc_start: 0.8306 (mp0) cc_final: 0.8073 (mp0) REVERT: W 425 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8285 (ttt90) REVERT: W 433 SER cc_start: 0.8576 (t) cc_final: 0.8353 (p) REVERT: X 37 GLU cc_start: 0.7798 (pp20) cc_final: 0.7527 (pp20) REVERT: X 94 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7723 (mt0) REVERT: X 125 PHE cc_start: 0.8812 (t80) cc_final: 0.8545 (t80) REVERT: X 140 TYR cc_start: 0.8794 (m-80) cc_final: 0.8586 (m-80) REVERT: X 192 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7720 (mm-30) REVERT: X 203 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6544 (tm-30) REVERT: X 282 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7905 (tm-30) REVERT: X 341 ASN cc_start: 0.8856 (p0) cc_final: 0.8501 (p0) REVERT: X 386 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8238 (tpp-160) REVERT: X 389 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.8048 (t) REVERT: X 390 VAL cc_start: 0.8573 (t) cc_final: 0.8250 (p) REVERT: Y 106 ILE cc_start: 0.8650 (pp) cc_final: 0.8180 (mp) REVERT: Y 115 GLU cc_start: 0.7810 (tp30) cc_final: 0.7509 (tp30) REVERT: Y 144 GLN cc_start: 0.7015 (mp10) cc_final: 0.6781 (mp10) REVERT: Y 184 VAL cc_start: 0.9124 (m) cc_final: 0.8884 (t) REVERT: Y 202 LEU cc_start: 0.8901 (mm) cc_final: 0.8625 (mp) REVERT: Y 261 ASP cc_start: 0.8140 (p0) cc_final: 0.7925 (p0) REVERT: Y 282 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8097 (tm-30) REVERT: Y 350 ARG cc_start: 0.8227 (mtm-85) cc_final: 0.7906 (mtp85) REVERT: Y 357 LYS cc_start: 0.8734 (mttm) cc_final: 0.8428 (mtmm) REVERT: Y 392 VAL cc_start: 0.8658 (t) cc_final: 0.8347 (p) REVERT: Q 957 THR cc_start: 0.7693 (p) cc_final: 0.7389 (t) REVERT: Q 1021 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: Q 1078 ARG cc_start: 0.8086 (mtm-85) cc_final: 0.7860 (mtm-85) REVERT: Q 1103 ASP cc_start: 0.8693 (p0) cc_final: 0.7877 (p0) REVERT: Q 1160 LYS cc_start: 0.7993 (ptpp) cc_final: 0.7709 (ptpp) REVERT: Q 1266 GLU cc_start: 0.7971 (mp0) cc_final: 0.7526 (mp0) REVERT: Q 1280 LYS cc_start: 0.8599 (ptpp) cc_final: 0.8329 (ptpp) REVERT: Q 1301 LEU cc_start: 0.8351 (tp) cc_final: 0.8014 (tt) REVERT: Q 1305 ASP cc_start: 0.8335 (m-30) cc_final: 0.7990 (m-30) REVERT: Q 1432 MET cc_start: 0.6345 (tpp) cc_final: 0.6100 (tpp) outliers start: 130 outliers final: 48 residues processed: 875 average time/residue: 1.6114 time to fit residues: 1608.4804 Evaluate side-chains 879 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 814 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 146 GLN Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain T residue 148 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 136 ILE Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 239 VAL Chi-restraints excluded: chain U residue 297 GLU Chi-restraints excluded: chain U residue 350 ARG Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 161 LYS Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 325 ASN Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 398 SER Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 134 GLU Chi-restraints excluded: chain W residue 233 LYS Chi-restraints excluded: chain W residue 338 LYS Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 373 GLN Chi-restraints excluded: chain W residue 425 ARG Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 386 ARG Chi-restraints excluded: chain X residue 389 THR Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 173 ASN Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 323 MET Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 440 VAL Chi-restraints excluded: chain Q residue 1021 ASP Chi-restraints excluded: chain Q residue 1150 LYS Chi-restraints excluded: chain Q residue 1203 LEU Chi-restraints excluded: chain Q residue 1233 ILE Chi-restraints excluded: chain Q residue 1324 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 327 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 177 optimal weight: 0.6980 chunk 145 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 231 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 332 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 312 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 65 ASN R 107 ASN R 633 GLN U 144 GLN U 237 HIS V 263 GLN V 314 ASN V 394 GLN V 417 GLN W 173 ASN X 271 GLN X 289 ASN X 325 ASN Y 49 GLN Y 310 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.120033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.099252 restraints weight = 44533.329| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.17 r_work: 0.3192 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29104 Z= 0.172 Angle : 0.595 8.653 39373 Z= 0.294 Chirality : 0.044 0.193 4620 Planarity : 0.005 0.195 5040 Dihedral : 7.117 125.810 4004 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.08 % Allowed : 26.35 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3618 helix: 0.92 (0.14), residues: 1518 sheet: 0.59 (0.19), residues: 672 loop : -1.04 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 280 HIS 0.004 0.001 HIS V 165 PHE 0.026 0.001 PHE R 691 TYR 0.027 0.002 TYR R 724 ARG 0.023 0.000 ARG X 180 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 1072) hydrogen bonds : angle 4.05111 ( 3135) covalent geometry : bond 0.00415 (29102) covalent geometry : angle 0.59510 (39373) Misc. bond : bond 0.00496 ( 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 950 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 821 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.8540 (p0) cc_final: 0.8111 (p0) REVERT: R 38 SER cc_start: 0.8527 (t) cc_final: 0.8296 (m) REVERT: R 70 PHE cc_start: 0.7774 (t80) cc_final: 0.7498 (t80) REVERT: R 95 GLN cc_start: 0.8523 (mt0) cc_final: 0.8215 (mt0) REVERT: R 112 GLU cc_start: 0.7917 (tt0) cc_final: 0.7483 (mt-10) REVERT: R 121 HIS cc_start: 0.8558 (OUTLIER) cc_final: 0.8114 (m-70) REVERT: R 193 ASP cc_start: 0.7726 (p0) cc_final: 0.7509 (p0) REVERT: R 238 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7955 (mtm) REVERT: R 241 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8615 (mp) REVERT: R 244 GLU cc_start: 0.7946 (tt0) cc_final: 0.7664 (tm-30) REVERT: R 246 MET cc_start: 0.8563 (ptt) cc_final: 0.8336 (ptt) REVERT: R 249 ASP cc_start: 0.8160 (m-30) cc_final: 0.7894 (m-30) REVERT: R 278 GLU cc_start: 0.7965 (tt0) cc_final: 0.7326 (tm-30) REVERT: R 617 GLU cc_start: 0.8252 (mp0) cc_final: 0.7972 (mp0) REVERT: R 643 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8117 (tm-30) REVERT: R 659 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7847 (mm-40) REVERT: S 77 LEU cc_start: 0.8714 (mp) cc_final: 0.8458 (mt) REVERT: S 80 LYS cc_start: 0.8696 (tmmt) cc_final: 0.8492 (tmmt) REVERT: S 159 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8096 (ptm160) REVERT: T 37 GLU cc_start: 0.7352 (pm20) cc_final: 0.7016 (pm20) REVERT: T 90 LEU cc_start: 0.8759 (mm) cc_final: 0.8542 (mt) REVERT: T 187 GLU cc_start: 0.7670 (tp30) cc_final: 0.7430 (tp30) REVERT: T 203 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: T 205 ASN cc_start: 0.8450 (m-40) cc_final: 0.7907 (m-40) REVERT: T 234 LYS cc_start: 0.8536 (mmmm) cc_final: 0.8268 (mmmm) REVERT: T 285 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8618 (mtt90) REVERT: T 386 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8402 (mpt180) REVERT: T 392 ARG cc_start: 0.8257 (mtm110) cc_final: 0.7928 (mtm-85) REVERT: U 32 ASP cc_start: 0.7978 (m-30) cc_final: 0.7713 (m-30) REVERT: U 71 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8419 (p) REVERT: U 110 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7508 (pp20) REVERT: U 143 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8597 (tt) REVERT: U 164 ASP cc_start: 0.8390 (m-30) cc_final: 0.8125 (m-30) REVERT: U 170 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7922 (tp30) REVERT: U 174 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7922 (mtpt) REVERT: U 255 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8527 (mp) REVERT: U 271 ASP cc_start: 0.8087 (m-30) cc_final: 0.7827 (m-30) REVERT: U 282 GLU cc_start: 0.8467 (tp30) cc_final: 0.8173 (tp30) REVERT: U 300 MET cc_start: 0.9135 (mmm) cc_final: 0.8877 (mmm) REVERT: V 36 ASP cc_start: 0.7725 (m-30) cc_final: 0.7271 (m-30) REVERT: V 42 LYS cc_start: 0.8223 (mtmm) cc_final: 0.7902 (tttm) REVERT: V 135 GLU cc_start: 0.7511 (tt0) cc_final: 0.7269 (tt0) REVERT: V 148 THR cc_start: 0.8756 (m) cc_final: 0.8504 (p) REVERT: V 154 ASN cc_start: 0.8015 (t0) cc_final: 0.7657 (t0) REVERT: V 203 GLU cc_start: 0.8081 (tt0) cc_final: 0.7811 (tt0) REVERT: V 298 GLN cc_start: 0.8090 (mp10) cc_final: 0.7817 (mp10) REVERT: W 36 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8143 (mm110) REVERT: W 177 ASP cc_start: 0.8547 (m-30) cc_final: 0.8285 (m-30) REVERT: W 283 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7479 (tm-30) REVERT: W 385 ASP cc_start: 0.8123 (m-30) cc_final: 0.7755 (m-30) REVERT: W 389 LYS cc_start: 0.8479 (mmmm) cc_final: 0.8051 (mmmm) REVERT: W 405 VAL cc_start: 0.7980 (t) cc_final: 0.7766 (m) REVERT: W 425 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8310 (ttt90) REVERT: X 37 GLU cc_start: 0.7814 (pp20) cc_final: 0.7561 (pp20) REVERT: X 94 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7691 (mp10) REVERT: X 135 GLU cc_start: 0.7656 (tt0) cc_final: 0.7351 (mt-10) REVERT: X 282 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7889 (tm-30) REVERT: X 336 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8664 (t) REVERT: X 341 ASN cc_start: 0.8853 (p0) cc_final: 0.8520 (p0) REVERT: X 386 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8295 (tpp-160) REVERT: X 389 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8107 (t) REVERT: X 390 VAL cc_start: 0.8613 (t) cc_final: 0.8294 (p) REVERT: X 444 LEU cc_start: 0.8488 (tp) cc_final: 0.8260 (tt) REVERT: Y 69 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7943 (mmt-90) REVERT: Y 81 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8242 (mtmt) REVERT: Y 106 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8234 (mp) REVERT: Y 115 GLU cc_start: 0.7791 (tp30) cc_final: 0.7509 (tp30) REVERT: Y 144 GLN cc_start: 0.7038 (mp10) cc_final: 0.6789 (mp10) REVERT: Y 184 VAL cc_start: 0.9122 (m) cc_final: 0.8902 (t) REVERT: Y 261 ASP cc_start: 0.8139 (p0) cc_final: 0.7933 (p0) REVERT: Y 350 ARG cc_start: 0.8215 (mtm-85) cc_final: 0.7942 (mtp85) REVERT: Y 392 VAL cc_start: 0.8679 (t) cc_final: 0.8369 (p) REVERT: Q 957 THR cc_start: 0.7807 (p) cc_final: 0.7509 (t) REVERT: Q 1021 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7655 (m-30) REVERT: Q 1073 LEU cc_start: 0.8945 (tp) cc_final: 0.8660 (tt) REVERT: Q 1078 ARG cc_start: 0.8081 (mtm-85) cc_final: 0.7763 (mtm-85) REVERT: Q 1103 ASP cc_start: 0.8700 (p0) cc_final: 0.7492 (p0) REVERT: Q 1139 GLU cc_start: 0.8141 (tp30) cc_final: 0.7921 (tp30) REVERT: Q 1160 LYS cc_start: 0.8028 (ptpp) cc_final: 0.7757 (ptpp) REVERT: Q 1266 GLU cc_start: 0.7977 (mp0) cc_final: 0.7529 (mp0) REVERT: Q 1280 LYS cc_start: 0.8616 (ptpp) cc_final: 0.8340 (ptpp) REVERT: Q 1301 LEU cc_start: 0.8415 (tp) cc_final: 0.8060 (tt) REVERT: Q 1302 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7561 (ttt90) REVERT: Q 1305 ASP cc_start: 0.8330 (m-30) cc_final: 0.8011 (m-30) REVERT: Q 1432 MET cc_start: 0.6192 (tpp) cc_final: 0.5975 (tpp) outliers start: 129 outliers final: 60 residues processed: 875 average time/residue: 1.6494 time to fit residues: 1652.8332 Evaluate side-chains 889 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 807 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 147 MET Chi-restraints excluded: chain S residue 159 ARG Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 148 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain T residue 285 ARG Chi-restraints excluded: chain T residue 318 ILE Chi-restraints excluded: chain T residue 364 ILE Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain T residue 398 SER Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 136 ILE Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 239 VAL Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 179 LEU Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 325 ASN Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 373 LEU Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 398 SER Chi-restraints excluded: chain V residue 400 LEU Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 134 GLU Chi-restraints excluded: chain W residue 233 LYS Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 336 ASN Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 373 GLN Chi-restraints excluded: chain W residue 425 ARG Chi-restraints excluded: chain W residue 455 GLN Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 243 ILE Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 324 LEU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 386 ARG Chi-restraints excluded: chain X residue 389 THR Chi-restraints excluded: chain Y residue 69 ARG Chi-restraints excluded: chain Y residue 81 LYS Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 238 THR Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 323 MET Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 374 GLU Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Q residue 983 THR Chi-restraints excluded: chain Q residue 1021 ASP Chi-restraints excluded: chain Q residue 1161 ASN Chi-restraints excluded: chain Q residue 1203 LEU Chi-restraints excluded: chain Q residue 1208 ARG Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1302 ARG Chi-restraints excluded: chain Q residue 1343 ILE Chi-restraints excluded: chain Q residue 1361 TRP Chi-restraints excluded: chain Q residue 1405 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 167 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 289 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 267 optimal weight: 0.3980 chunk 190 optimal weight: 0.0980 chunk 104 optimal weight: 0.0370 chunk 317 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 200 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 65 ASN R 109 ASN R 146 GLN R 213 ASN R 633 GLN R 635 GLN S 141 GLN U 144 GLN V 51 GLN V 263 GLN V 394 GLN V 417 GLN W 173 ASN X 51 GLN X 271 GLN X 289 ASN X 325 ASN Y 49 GLN Y 310 ASN Q1244 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.121624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.100888 restraints weight = 44010.516| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.15 r_work: 0.3222 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29104 Z= 0.115 Angle : 0.559 8.051 39373 Z= 0.275 Chirality : 0.043 0.202 4620 Planarity : 0.004 0.090 5040 Dihedral : 6.731 119.379 4004 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.89 % Allowed : 27.08 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3618 helix: 1.18 (0.14), residues: 1516 sheet: 0.63 (0.20), residues: 672 loop : -0.94 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 280 HIS 0.005 0.001 HIS V 165 PHE 0.023 0.001 PHE R 691 TYR 0.017 0.001 TYR X 295 ARG 0.019 0.000 ARG X 180 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 1072) hydrogen bonds : angle 3.89231 ( 3135) covalent geometry : bond 0.00267 (29102) covalent geometry : angle 0.55855 (39373) Misc. bond : bond 0.00318 ( 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 938 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 815 time to evaluate : 3.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.8541 (p0) cc_final: 0.8116 (p0) REVERT: R 38 SER cc_start: 0.8503 (t) cc_final: 0.8266 (m) REVERT: R 70 PHE cc_start: 0.7787 (t80) cc_final: 0.7496 (t80) REVERT: R 95 GLN cc_start: 0.8495 (mt0) cc_final: 0.8159 (mt0) REVERT: R 101 ASP cc_start: 0.7944 (t70) cc_final: 0.7522 (p0) REVERT: R 112 GLU cc_start: 0.7900 (tt0) cc_final: 0.7473 (mt-10) REVERT: R 121 HIS cc_start: 0.8563 (OUTLIER) cc_final: 0.8111 (m-70) REVERT: R 193 ASP cc_start: 0.7776 (p0) cc_final: 0.7539 (p0) REVERT: R 238 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7961 (mtm) REVERT: R 241 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8609 (mp) REVERT: R 244 GLU cc_start: 0.7894 (tt0) cc_final: 0.7655 (tm-30) REVERT: R 249 ASP cc_start: 0.8141 (m-30) cc_final: 0.7907 (m-30) REVERT: R 278 GLU cc_start: 0.7905 (tt0) cc_final: 0.7336 (tm-30) REVERT: R 609 GLN cc_start: 0.8051 (mt0) cc_final: 0.7759 (mt0) REVERT: R 617 GLU cc_start: 0.8163 (mp0) cc_final: 0.7876 (mp0) REVERT: R 643 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8073 (tm-30) REVERT: R 719 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7181 (mpp80) REVERT: S 77 LEU cc_start: 0.8651 (mp) cc_final: 0.8379 (mt) REVERT: T 37 GLU cc_start: 0.7286 (pm20) cc_final: 0.6982 (pm20) REVERT: T 82 SER cc_start: 0.8978 (p) cc_final: 0.8738 (t) REVERT: T 90 LEU cc_start: 0.8755 (mm) cc_final: 0.8536 (mt) REVERT: T 187 GLU cc_start: 0.7651 (tp30) cc_final: 0.7400 (tp30) REVERT: T 203 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7654 (tm-30) REVERT: T 205 ASN cc_start: 0.8481 (m-40) cc_final: 0.7919 (m-40) REVERT: T 206 THR cc_start: 0.8698 (m) cc_final: 0.8206 (p) REVERT: T 234 LYS cc_start: 0.8528 (mmmm) cc_final: 0.8266 (mmmm) REVERT: T 332 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7712 (tp) REVERT: T 386 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8430 (mpt180) REVERT: T 392 ARG cc_start: 0.8227 (mtm110) cc_final: 0.7911 (mtm-85) REVERT: T 454 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8378 (mttt) REVERT: U 32 ASP cc_start: 0.7942 (m-30) cc_final: 0.7697 (m-30) REVERT: U 110 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7498 (pp20) REVERT: U 135 LEU cc_start: 0.8787 (mt) cc_final: 0.8534 (mm) REVERT: U 143 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.7798 (tt) REVERT: U 170 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7896 (tp30) REVERT: U 174 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7898 (mtpt) REVERT: U 255 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8564 (mp) REVERT: U 271 ASP cc_start: 0.8092 (m-30) cc_final: 0.7852 (m-30) REVERT: U 282 GLU cc_start: 0.8463 (tp30) cc_final: 0.8116 (tp30) REVERT: U 300 MET cc_start: 0.9119 (mmm) cc_final: 0.8877 (mmm) REVERT: U 350 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.7842 (mtp85) REVERT: V 36 ASP cc_start: 0.7679 (m-30) cc_final: 0.7212 (m-30) REVERT: V 42 LYS cc_start: 0.8234 (mtmm) cc_final: 0.7917 (tttm) REVERT: V 135 GLU cc_start: 0.7492 (tt0) cc_final: 0.7270 (tt0) REVERT: V 148 THR cc_start: 0.8746 (m) cc_final: 0.8521 (p) REVERT: V 154 ASN cc_start: 0.7966 (t0) cc_final: 0.7610 (t0) REVERT: V 203 GLU cc_start: 0.8017 (tt0) cc_final: 0.7780 (tt0) REVERT: V 236 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: V 298 GLN cc_start: 0.8061 (mp10) cc_final: 0.7789 (mp10) REVERT: V 428 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8746 (t) REVERT: W 177 ASP cc_start: 0.8555 (m-30) cc_final: 0.8282 (m-30) REVERT: W 385 ASP cc_start: 0.8071 (m-30) cc_final: 0.7624 (m-30) REVERT: W 419 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7732 (mm-30) REVERT: W 425 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8309 (ttt90) REVERT: X 37 GLU cc_start: 0.7808 (pp20) cc_final: 0.7551 (pp20) REVERT: X 94 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7670 (mt0) REVERT: X 135 GLU cc_start: 0.7597 (tt0) cc_final: 0.7312 (mt-10) REVERT: X 282 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7880 (tm-30) REVERT: X 341 ASN cc_start: 0.8811 (p0) cc_final: 0.8498 (p0) REVERT: X 386 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8296 (tpp-160) REVERT: X 390 VAL cc_start: 0.8581 (t) cc_final: 0.8233 (p) REVERT: Y 106 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8250 (mp) REVERT: Y 144 GLN cc_start: 0.7069 (mp10) cc_final: 0.6808 (mp10) REVERT: Y 184 VAL cc_start: 0.9152 (m) cc_final: 0.8894 (t) REVERT: Y 261 ASP cc_start: 0.8121 (p0) cc_final: 0.7917 (p0) REVERT: Y 350 ARG cc_start: 0.8135 (mtm-85) cc_final: 0.7873 (mtm-85) REVERT: Y 392 VAL cc_start: 0.8621 (t) cc_final: 0.8287 (p) REVERT: Q 957 THR cc_start: 0.7817 (p) cc_final: 0.7525 (t) REVERT: Q 1021 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: Q 1097 ASN cc_start: 0.8434 (p0) cc_final: 0.8219 (p0) REVERT: Q 1103 ASP cc_start: 0.8671 (p0) cc_final: 0.7461 (p0) REVERT: Q 1139 GLU cc_start: 0.8095 (tp30) cc_final: 0.7877 (tp30) REVERT: Q 1160 LYS cc_start: 0.8025 (ptpp) cc_final: 0.7763 (ptpp) REVERT: Q 1239 ASP cc_start: 0.8134 (t70) cc_final: 0.7929 (t70) REVERT: Q 1241 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8378 (tp) REVERT: Q 1266 GLU cc_start: 0.7945 (mp0) cc_final: 0.7521 (mp0) REVERT: Q 1280 LYS cc_start: 0.8564 (ptpp) cc_final: 0.8311 (ptpp) REVERT: Q 1301 LEU cc_start: 0.8438 (tp) cc_final: 0.8040 (tt) REVERT: Q 1305 ASP cc_start: 0.8262 (m-30) cc_final: 0.7930 (m-30) REVERT: Q 1432 MET cc_start: 0.6213 (tpp) cc_final: 0.5998 (tpp) outliers start: 123 outliers final: 52 residues processed: 867 average time/residue: 1.6203 time to fit residues: 1601.8951 Evaluate side-chains 874 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 802 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 147 MET Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 148 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 136 ILE Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 346 ASP Chi-restraints excluded: chain U residue 350 ARG Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 188 SER Chi-restraints excluded: chain V residue 236 GLU Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 325 ASN Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 398 SER Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain W residue 63 ASN Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 110 GLU Chi-restraints excluded: chain W residue 215 MET Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 373 GLN Chi-restraints excluded: chain W residue 421 GLU Chi-restraints excluded: chain W residue 425 ARG Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 324 LEU Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 386 ARG Chi-restraints excluded: chain X residue 454 LYS Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 183 LYS Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 323 MET Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 374 GLU Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 440 VAL Chi-restraints excluded: chain Q residue 983 THR Chi-restraints excluded: chain Q residue 1021 ASP Chi-restraints excluded: chain Q residue 1091 GLU Chi-restraints excluded: chain Q residue 1161 ASN Chi-restraints excluded: chain Q residue 1203 LEU Chi-restraints excluded: chain Q residue 1241 LEU Chi-restraints excluded: chain Q residue 1405 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 165 optimal weight: 0.9980 chunk 300 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 306 optimal weight: 0.6980 chunk 268 optimal weight: 3.9990 chunk 79 optimal weight: 0.0040 chunk 115 optimal weight: 1.9990 chunk 318 optimal weight: 0.0670 chunk 345 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 overall best weight: 0.3530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 633 GLN U 155 GLN V 51 GLN V 263 GLN V 394 GLN V 417 GLN X 271 GLN X 289 ASN X 325 ASN X 440 ASN Y 49 GLN Y 310 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.122171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.101436 restraints weight = 44118.469| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.15 r_work: 0.3228 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29104 Z= 0.109 Angle : 0.558 7.831 39373 Z= 0.274 Chirality : 0.042 0.208 4620 Planarity : 0.004 0.068 5040 Dihedral : 6.523 117.857 4004 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.86 % Allowed : 27.74 % Favored : 68.40 % 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: 0.48 (0.14), residues: 3618 helix: 1.30 (0.14), residues: 1521 sheet: 0.65 (0.20), residues: 662 loop : -0.88 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 280 HIS 0.006 0.001 HIS V 165 PHE 0.023 0.001 PHE R 691 TYR 0.034 0.001 TYR R 724 ARG 0.012 0.000 ARG X 180 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 1072) hydrogen bonds : angle 3.81417 ( 3135) covalent geometry : bond 0.00255 (29102) covalent geometry : angle 0.55758 (39373) Misc. bond : bond 0.00455 ( 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 928 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 806 time to evaluate : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.8556 (p0) cc_final: 0.8115 (p0) REVERT: R 38 SER cc_start: 0.8491 (t) cc_final: 0.8229 (m) REVERT: R 70 PHE cc_start: 0.7764 (t80) cc_final: 0.7455 (t80) REVERT: R 75 LEU cc_start: 0.8493 (mm) cc_final: 0.8068 (tm) REVERT: R 95 GLN cc_start: 0.8521 (mt0) cc_final: 0.8146 (mt0) REVERT: R 101 ASP cc_start: 0.7943 (t70) cc_final: 0.7512 (p0) REVERT: R 112 GLU cc_start: 0.7865 (tt0) cc_final: 0.7457 (mt-10) REVERT: R 121 HIS cc_start: 0.8578 (OUTLIER) cc_final: 0.8159 (m-70) REVERT: R 146 GLN cc_start: 0.7592 (mm110) cc_final: 0.7365 (mm-40) REVERT: R 193 ASP cc_start: 0.7771 (p0) cc_final: 0.7534 (p0) REVERT: R 238 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7932 (mtm) REVERT: R 241 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8556 (mp) REVERT: R 242 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.6982 (mp10) REVERT: R 244 GLU cc_start: 0.7886 (tt0) cc_final: 0.7629 (tm-30) REVERT: R 249 ASP cc_start: 0.8191 (m-30) cc_final: 0.7928 (m-30) REVERT: R 278 GLU cc_start: 0.7904 (tt0) cc_final: 0.7258 (tm-30) REVERT: R 609 GLN cc_start: 0.8066 (mt0) cc_final: 0.7752 (mt0) REVERT: R 617 GLU cc_start: 0.8163 (mp0) cc_final: 0.7940 (mp0) REVERT: R 643 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8068 (tm-30) REVERT: R 719 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7176 (mpp80) REVERT: T 82 SER cc_start: 0.8963 (p) cc_final: 0.8730 (t) REVERT: T 90 LEU cc_start: 0.8720 (mm) cc_final: 0.8503 (mt) REVERT: T 119 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: T 123 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7903 (mt-10) REVERT: T 181 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7891 (mp) REVERT: T 187 GLU cc_start: 0.7623 (tp30) cc_final: 0.7099 (tp30) REVERT: T 203 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: T 205 ASN cc_start: 0.8447 (m-40) cc_final: 0.7890 (m-40) REVERT: T 386 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8361 (mpt180) REVERT: T 392 ARG cc_start: 0.8216 (mtm110) cc_final: 0.7897 (mtm-85) REVERT: U 32 ASP cc_start: 0.7965 (m-30) cc_final: 0.7693 (m-30) REVERT: U 71 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8430 (p) REVERT: U 110 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7470 (pp20) REVERT: U 135 LEU cc_start: 0.8763 (mt) cc_final: 0.8490 (mm) REVERT: U 170 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7903 (tp30) REVERT: U 174 LYS cc_start: 0.8074 (mtpt) cc_final: 0.7851 (mtpt) REVERT: U 233 LYS cc_start: 0.8333 (mmmt) cc_final: 0.8124 (mmmt) REVERT: U 255 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8495 (mp) REVERT: U 271 ASP cc_start: 0.8084 (m-30) cc_final: 0.7843 (m-30) REVERT: U 282 GLU cc_start: 0.8441 (tp30) cc_final: 0.8106 (tp30) REVERT: U 300 MET cc_start: 0.9123 (mmm) cc_final: 0.8872 (mmm) REVERT: U 350 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.7811 (mtp85) REVERT: V 36 ASP cc_start: 0.7714 (m-30) cc_final: 0.7229 (m-30) REVERT: V 42 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7914 (tttm) REVERT: V 135 GLU cc_start: 0.7467 (tt0) cc_final: 0.7253 (tt0) REVERT: V 148 THR cc_start: 0.8753 (m) cc_final: 0.8518 (p) REVERT: V 154 ASN cc_start: 0.7976 (t0) cc_final: 0.7618 (t0) REVERT: V 203 GLU cc_start: 0.8076 (tt0) cc_final: 0.7826 (tt0) REVERT: V 269 MET cc_start: 0.8868 (mmp) cc_final: 0.8665 (mmm) REVERT: V 298 GLN cc_start: 0.8098 (mp10) cc_final: 0.7866 (mp10) REVERT: V 428 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8729 (t) REVERT: V 451 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7103 (mtp180) REVERT: W 177 ASP cc_start: 0.8558 (m-30) cc_final: 0.8278 (m-30) REVERT: W 228 GLU cc_start: 0.8226 (mm-30) cc_final: 0.8006 (tp30) REVERT: W 374 GLU cc_start: 0.7513 (tp30) cc_final: 0.7281 (tt0) REVERT: W 385 ASP cc_start: 0.8117 (m-30) cc_final: 0.7742 (m-30) REVERT: W 389 LYS cc_start: 0.8518 (tttp) cc_final: 0.8318 (tttp) REVERT: W 419 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7561 (mp0) REVERT: W 425 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8266 (ttt90) REVERT: X 37 GLU cc_start: 0.7812 (pp20) cc_final: 0.7535 (pp20) REVERT: X 94 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7644 (mt0) REVERT: X 282 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7816 (tm-30) REVERT: X 341 ASN cc_start: 0.8803 (p0) cc_final: 0.8513 (p0) REVERT: Y 23 HIS cc_start: 0.8544 (p90) cc_final: 0.8311 (p-80) REVERT: Y 106 ILE cc_start: 0.8637 (pp) cc_final: 0.8290 (mp) REVERT: Y 144 GLN cc_start: 0.7040 (mp10) cc_final: 0.6756 (mp10) REVERT: Y 184 VAL cc_start: 0.9140 (m) cc_final: 0.8871 (t) REVERT: Y 261 ASP cc_start: 0.8185 (p0) cc_final: 0.7983 (p0) REVERT: Y 317 PHE cc_start: 0.8841 (m-80) cc_final: 0.8518 (m-80) REVERT: Y 350 ARG cc_start: 0.8095 (mtm-85) cc_final: 0.7792 (mtm-85) REVERT: Y 392 VAL cc_start: 0.8574 (t) cc_final: 0.8242 (p) REVERT: Q 957 THR cc_start: 0.7790 (p) cc_final: 0.7489 (t) REVERT: Q 1021 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7568 (m-30) REVERT: Q 1097 ASN cc_start: 0.8411 (p0) cc_final: 0.8174 (p0) REVERT: Q 1103 ASP cc_start: 0.8639 (p0) cc_final: 0.7820 (p0) REVERT: Q 1160 LYS cc_start: 0.8120 (ptpp) cc_final: 0.7829 (ptpp) REVERT: Q 1167 PHE cc_start: 0.8390 (p90) cc_final: 0.8086 (p90) REVERT: Q 1241 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8274 (tp) REVERT: Q 1266 GLU cc_start: 0.7952 (mp0) cc_final: 0.7522 (mp0) REVERT: Q 1280 LYS cc_start: 0.8573 (ptpp) cc_final: 0.8306 (ptpp) REVERT: Q 1301 LEU cc_start: 0.8393 (tp) cc_final: 0.7998 (tt) REVERT: Q 1305 ASP cc_start: 0.8270 (m-30) cc_final: 0.7929 (m-30) outliers start: 122 outliers final: 63 residues processed: 861 average time/residue: 1.6280 time to fit residues: 1624.7754 Evaluate side-chains 883 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 800 time to evaluate : 3.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 181 ASN Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 591 LEU Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 147 MET Chi-restraints excluded: chain T residue 119 GLU Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 181 LEU Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 136 ILE Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 239 VAL Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 350 ARG Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 458 ILE Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 188 SER Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 325 ASN Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 398 SER Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain V residue 451 ARG Chi-restraints excluded: chain W residue 63 ASN Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 110 GLU Chi-restraints excluded: chain W residue 131 GLU Chi-restraints excluded: chain W residue 134 GLU Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 373 GLN Chi-restraints excluded: chain W residue 425 ARG Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 245 GLN Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 324 LEU Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 183 LYS Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 323 MET Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 361 GLU Chi-restraints excluded: chain Y residue 374 GLU Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 983 THR Chi-restraints excluded: chain Q residue 1021 ASP Chi-restraints excluded: chain Q residue 1091 GLU Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1131 LEU Chi-restraints excluded: chain Q residue 1161 ASN Chi-restraints excluded: chain Q residue 1162 THR Chi-restraints excluded: chain Q residue 1203 LEU Chi-restraints excluded: chain Q residue 1241 LEU Chi-restraints excluded: chain Q residue 1361 TRP Chi-restraints excluded: chain Q residue 1405 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 187 optimal weight: 1.9990 chunk 300 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 307 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 332 optimal weight: 0.9990 chunk 269 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 306 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 633 GLN S 141 GLN V 263 GLN V 394 GLN V 417 GLN W 173 ASN X 271 GLN X 289 ASN X 325 ASN X 440 ASN Y 49 GLN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.120503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.099752 restraints weight = 44125.831| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.14 r_work: 0.3202 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29104 Z= 0.174 Angle : 0.611 12.614 39373 Z= 0.300 Chirality : 0.044 0.219 4620 Planarity : 0.006 0.349 5040 Dihedral : 6.695 119.577 4004 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.80 % Allowed : 28.22 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3618 helix: 1.25 (0.14), residues: 1524 sheet: 0.63 (0.20), residues: 662 loop : -0.92 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 280 HIS 0.007 0.001 HIS V 165 PHE 0.026 0.001 PHE R 691 TYR 0.026 0.002 TYR R 724 ARG 0.018 0.001 ARG X 180 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 1072) hydrogen bonds : angle 3.91677 ( 3135) covalent geometry : bond 0.00418 (29102) covalent geometry : angle 0.61051 (39373) Misc. bond : bond 0.00599 ( 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 928 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 808 time to evaluate : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.8556 (p0) cc_final: 0.8116 (p0) REVERT: R 38 SER cc_start: 0.8502 (t) cc_final: 0.8242 (m) REVERT: R 70 PHE cc_start: 0.7728 (t80) cc_final: 0.7403 (t80) REVERT: R 75 LEU cc_start: 0.8501 (mm) cc_final: 0.8085 (tm) REVERT: R 95 GLN cc_start: 0.8566 (mt0) cc_final: 0.8167 (mt0) REVERT: R 112 GLU cc_start: 0.7914 (tt0) cc_final: 0.7520 (mt-10) REVERT: R 121 HIS cc_start: 0.8578 (OUTLIER) cc_final: 0.8180 (m-70) REVERT: R 146 GLN cc_start: 0.7682 (mm110) cc_final: 0.7426 (mm-40) REVERT: R 193 ASP cc_start: 0.7773 (p0) cc_final: 0.7519 (p0) REVERT: R 238 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7976 (mtm) REVERT: R 241 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8581 (mp) REVERT: R 242 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.6995 (mp10) REVERT: R 244 GLU cc_start: 0.7914 (tt0) cc_final: 0.7649 (tm-30) REVERT: R 249 ASP cc_start: 0.8204 (m-30) cc_final: 0.7890 (m-30) REVERT: R 278 GLU cc_start: 0.7956 (tt0) cc_final: 0.7317 (tm-30) REVERT: R 609 GLN cc_start: 0.8087 (mt0) cc_final: 0.7757 (mt0) REVERT: R 617 GLU cc_start: 0.8299 (mp0) cc_final: 0.8042 (mp0) REVERT: R 643 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8069 (tm-30) REVERT: R 719 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7213 (mpp80) REVERT: T 90 LEU cc_start: 0.8728 (mm) cc_final: 0.8516 (mt) REVERT: T 119 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: T 123 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8023 (mt-10) REVERT: T 187 GLU cc_start: 0.7639 (tp30) cc_final: 0.7342 (tp30) REVERT: T 203 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7661 (tm-30) REVERT: T 205 ASN cc_start: 0.8453 (m-40) cc_final: 0.8189 (m-40) REVERT: T 332 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7733 (tp) REVERT: T 355 SER cc_start: 0.8374 (t) cc_final: 0.8154 (p) REVERT: T 386 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8389 (mpt180) REVERT: T 392 ARG cc_start: 0.8215 (mtm110) cc_final: 0.7914 (mtm-85) REVERT: U 32 ASP cc_start: 0.7973 (m-30) cc_final: 0.7690 (m-30) REVERT: U 71 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8417 (p) REVERT: U 110 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7400 (pp20) REVERT: U 170 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7914 (tp30) REVERT: U 174 LYS cc_start: 0.8096 (mtpt) cc_final: 0.7873 (mtpt) REVERT: U 255 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8474 (mp) REVERT: U 271 ASP cc_start: 0.8105 (m-30) cc_final: 0.7860 (m-30) REVERT: U 282 GLU cc_start: 0.8432 (tp30) cc_final: 0.8079 (tp30) REVERT: U 350 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.7818 (mtp85) REVERT: U 455 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: V 36 ASP cc_start: 0.7747 (m-30) cc_final: 0.7291 (m-30) REVERT: V 42 LYS cc_start: 0.8204 (mtmm) cc_final: 0.7827 (tttm) REVERT: V 135 GLU cc_start: 0.7492 (tt0) cc_final: 0.7256 (tt0) REVERT: V 148 THR cc_start: 0.8772 (m) cc_final: 0.8522 (p) REVERT: V 154 ASN cc_start: 0.8015 (t0) cc_final: 0.7662 (t0) REVERT: V 203 GLU cc_start: 0.8105 (tt0) cc_final: 0.7874 (tt0) REVERT: V 298 GLN cc_start: 0.8176 (mp10) cc_final: 0.7926 (mp10) REVERT: V 428 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8730 (t) REVERT: V 451 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7095 (mtp180) REVERT: W 177 ASP cc_start: 0.8558 (m-30) cc_final: 0.8287 (m-30) REVERT: W 228 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8045 (tp30) REVERT: W 385 ASP cc_start: 0.8127 (m-30) cc_final: 0.7740 (m-30) REVERT: W 389 LYS cc_start: 0.8520 (tttp) cc_final: 0.8320 (tttp) REVERT: W 419 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7506 (mp0) REVERT: W 425 ARG cc_start: 0.8603 (ttt90) cc_final: 0.8312 (ttt90) REVERT: X 37 GLU cc_start: 0.7833 (pp20) cc_final: 0.7548 (pp20) REVERT: X 94 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7613 (mp10) REVERT: X 282 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7862 (tm-30) REVERT: X 341 ASN cc_start: 0.8830 (p0) cc_final: 0.8558 (p0) REVERT: X 390 VAL cc_start: 0.8520 (t) cc_final: 0.8232 (p) REVERT: X 396 GLU cc_start: 0.7334 (tm-30) cc_final: 0.6910 (tm-30) REVERT: Y 81 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8318 (mtmt) REVERT: Y 106 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8313 (mp) REVERT: Y 115 GLU cc_start: 0.7762 (tp30) cc_final: 0.7495 (tp30) REVERT: Y 144 GLN cc_start: 0.7055 (mp10) cc_final: 0.6766 (mp10) REVERT: Y 184 VAL cc_start: 0.9137 (m) cc_final: 0.8884 (t) REVERT: Y 202 LEU cc_start: 0.8985 (mm) cc_final: 0.8750 (mp) REVERT: Y 350 ARG cc_start: 0.8136 (mtm-85) cc_final: 0.7810 (mtp85) REVERT: Y 392 VAL cc_start: 0.8650 (t) cc_final: 0.8343 (p) REVERT: Q 957 THR cc_start: 0.7758 (p) cc_final: 0.7493 (t) REVERT: Q 1021 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7566 (m-30) REVERT: Q 1073 LEU cc_start: 0.8921 (tp) cc_final: 0.8651 (tt) REVERT: Q 1097 ASN cc_start: 0.8439 (p0) cc_final: 0.8197 (p0) REVERT: Q 1103 ASP cc_start: 0.8676 (p0) cc_final: 0.7480 (p0) REVERT: Q 1139 GLU cc_start: 0.8172 (tp30) cc_final: 0.7930 (tp30) REVERT: Q 1160 LYS cc_start: 0.8187 (ptpp) cc_final: 0.7902 (ptpp) REVERT: Q 1204 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.8381 (t0) REVERT: Q 1239 ASP cc_start: 0.8159 (t70) cc_final: 0.7921 (t70) REVERT: Q 1266 GLU cc_start: 0.7974 (mp0) cc_final: 0.7526 (mp0) REVERT: Q 1280 LYS cc_start: 0.8599 (ptpp) cc_final: 0.8331 (ptpp) REVERT: Q 1301 LEU cc_start: 0.8368 (tp) cc_final: 0.7975 (tt) REVERT: Q 1305 ASP cc_start: 0.8300 (m-30) cc_final: 0.7960 (m-30) REVERT: Q 1432 MET cc_start: 0.5793 (tpp) cc_final: 0.5491 (tpp) outliers start: 120 outliers final: 64 residues processed: 862 average time/residue: 1.5852 time to fit residues: 1561.0161 Evaluate side-chains 893 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 807 time to evaluate : 3.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 69 LYS Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 591 LEU Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain R residue 750 THR Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain T residue 119 GLU Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 148 THR Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 362 ASP Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 136 ILE Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 239 VAL Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 350 ARG Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 455 GLN Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 188 SER Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 398 SER Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain V residue 451 ARG Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 131 GLU Chi-restraints excluded: chain W residue 134 GLU Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain W residue 215 MET Chi-restraints excluded: chain W residue 233 LYS Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 373 GLN Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 156 LEU 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 265 VAL Chi-restraints excluded: chain X residue 324 LEU Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain Y residue 81 LYS Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 183 LYS Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 323 MET Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 361 GLU Chi-restraints excluded: chain Y residue 374 GLU Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 440 VAL Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 1021 ASP Chi-restraints excluded: chain Q residue 1091 GLU Chi-restraints excluded: chain Q residue 1150 LYS Chi-restraints excluded: chain Q residue 1161 ASN Chi-restraints excluded: chain Q residue 1162 THR Chi-restraints excluded: chain Q residue 1203 LEU Chi-restraints excluded: chain Q residue 1204 ASN Chi-restraints excluded: chain Q residue 1343 ILE Chi-restraints excluded: chain Q residue 1361 TRP Chi-restraints excluded: chain Q residue 1405 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 160 optimal weight: 0.9980 chunk 291 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 254 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 43 optimal weight: 0.0040 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 218 optimal weight: 0.7980 chunk 245 optimal weight: 3.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 633 GLN T 165 HIS V 263 GLN V 394 GLN V 417 GLN W 173 ASN X 271 GLN X 289 ASN X 325 ASN X 440 ASN Y 49 GLN ** Y 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.120585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.099860 restraints weight = 44149.088| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.15 r_work: 0.3205 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29104 Z= 0.155 Angle : 0.603 10.546 39373 Z= 0.296 Chirality : 0.044 0.221 4620 Planarity : 0.004 0.059 5040 Dihedral : 6.625 118.449 4004 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.26 % Allowed : 29.26 % Favored : 67.48 % 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: 0.43 (0.14), residues: 3618 helix: 1.26 (0.14), residues: 1521 sheet: 0.64 (0.20), residues: 660 loop : -0.92 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 280 HIS 0.007 0.001 HIS V 165 PHE 0.024 0.001 PHE R 691 TYR 0.020 0.002 TYR X 295 ARG 0.010 0.000 ARG Y 38 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 1072) hydrogen bonds : angle 3.90032 ( 3135) covalent geometry : bond 0.00373 (29102) covalent geometry : angle 0.60295 (39373) Misc. bond : bond 0.00159 ( 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 931 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 828 time to evaluate : 3.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.8551 (p0) cc_final: 0.8114 (p0) REVERT: R 38 SER cc_start: 0.8482 (t) cc_final: 0.8222 (m) REVERT: R 70 PHE cc_start: 0.7710 (t80) cc_final: 0.7374 (t80) REVERT: R 75 LEU cc_start: 0.8508 (mm) cc_final: 0.8095 (tm) REVERT: R 95 GLN cc_start: 0.8553 (mt0) cc_final: 0.8172 (mt0) REVERT: R 101 ASP cc_start: 0.7963 (t70) cc_final: 0.7475 (p0) REVERT: R 112 GLU cc_start: 0.7902 (tt0) cc_final: 0.7503 (mt-10) REVERT: R 113 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7297 (tt0) REVERT: R 121 HIS cc_start: 0.8577 (OUTLIER) cc_final: 0.8169 (m-70) REVERT: R 146 GLN cc_start: 0.7718 (mm110) cc_final: 0.7438 (mm-40) REVERT: R 193 ASP cc_start: 0.7774 (p0) cc_final: 0.7518 (p0) REVERT: R 238 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7988 (mtm) REVERT: R 241 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8585 (mp) REVERT: R 242 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7005 (mp10) REVERT: R 244 GLU cc_start: 0.7907 (tt0) cc_final: 0.7646 (tm-30) REVERT: R 249 ASP cc_start: 0.8194 (m-30) cc_final: 0.7874 (m-30) REVERT: R 278 GLU cc_start: 0.7936 (tt0) cc_final: 0.7370 (tm-30) REVERT: R 609 GLN cc_start: 0.8091 (mt0) cc_final: 0.7765 (mt0) REVERT: R 617 GLU cc_start: 0.8247 (mp0) cc_final: 0.7980 (mp0) REVERT: R 643 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8070 (tm-30) REVERT: R 719 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7208 (mpp80) REVERT: T 90 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8486 (mt) REVERT: T 119 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: T 123 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8032 (mt-10) REVERT: T 187 GLU cc_start: 0.7625 (tp30) cc_final: 0.7307 (tp30) REVERT: T 203 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: T 205 ASN cc_start: 0.8452 (m-40) cc_final: 0.8168 (m-40) REVERT: T 332 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7740 (tp) REVERT: T 355 SER cc_start: 0.8368 (t) cc_final: 0.8148 (p) REVERT: T 386 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8378 (mpt180) REVERT: T 392 ARG cc_start: 0.8233 (mtm110) cc_final: 0.7937 (mtm-85) REVERT: T 454 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8365 (mtpp) REVERT: U 32 ASP cc_start: 0.7947 (m-30) cc_final: 0.7672 (m-30) REVERT: U 71 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8431 (p) REVERT: U 164 ASP cc_start: 0.8456 (m-30) cc_final: 0.8251 (m-30) REVERT: U 170 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7903 (tp30) REVERT: U 174 LYS cc_start: 0.8096 (mtpt) cc_final: 0.7874 (mtpt) REVERT: U 255 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8467 (mp) REVERT: U 271 ASP cc_start: 0.8075 (m-30) cc_final: 0.7836 (m-30) REVERT: U 282 GLU cc_start: 0.8425 (tp30) cc_final: 0.8089 (tp30) REVERT: U 350 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.7836 (mtp85) REVERT: V 42 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7782 (tttm) REVERT: V 135 GLU cc_start: 0.7516 (tt0) cc_final: 0.7277 (tt0) REVERT: V 148 THR cc_start: 0.8780 (m) cc_final: 0.8525 (p) REVERT: V 154 ASN cc_start: 0.8000 (t0) cc_final: 0.7630 (t0) REVERT: V 180 ARG cc_start: 0.8837 (ttp80) cc_final: 0.8602 (ttp80) REVERT: V 203 GLU cc_start: 0.8103 (tt0) cc_final: 0.7901 (tt0) REVERT: V 298 GLN cc_start: 0.8168 (mp10) cc_final: 0.7919 (mp10) REVERT: V 428 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8719 (t) REVERT: V 451 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7047 (mtp180) REVERT: W 36 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8153 (mm110) REVERT: W 177 ASP cc_start: 0.8560 (m-30) cc_final: 0.8283 (m-30) REVERT: W 374 GLU cc_start: 0.7553 (tp30) cc_final: 0.7269 (tt0) REVERT: W 385 ASP cc_start: 0.8123 (m-30) cc_final: 0.7734 (m-30) REVERT: W 419 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7495 (mp0) REVERT: W 425 ARG cc_start: 0.8619 (ttt90) cc_final: 0.8336 (ttt90) REVERT: X 37 GLU cc_start: 0.7839 (pp20) cc_final: 0.7549 (pp20) REVERT: X 94 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7587 (mp10) REVERT: X 135 GLU cc_start: 0.7599 (tt0) cc_final: 0.7287 (mt-10) REVERT: X 221 GLU cc_start: 0.7689 (tt0) cc_final: 0.7456 (tm-30) REVERT: X 232 LEU cc_start: 0.9060 (tp) cc_final: 0.8849 (mm) REVERT: X 282 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7840 (tm-30) REVERT: X 341 ASN cc_start: 0.8823 (p0) cc_final: 0.8552 (p0) REVERT: X 390 VAL cc_start: 0.8509 (t) cc_final: 0.8215 (p) REVERT: X 396 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6857 (tm-30) REVERT: Y 106 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8328 (mp) REVERT: Y 115 GLU cc_start: 0.7732 (tp30) cc_final: 0.7474 (tp30) REVERT: Y 144 GLN cc_start: 0.7035 (mp10) cc_final: 0.6743 (mp10) REVERT: Y 184 VAL cc_start: 0.9115 (m) cc_final: 0.8904 (t) REVERT: Y 202 LEU cc_start: 0.8999 (mm) cc_final: 0.8774 (mp) REVERT: Y 350 ARG cc_start: 0.8141 (mtm-85) cc_final: 0.7861 (mtm-85) REVERT: Y 392 VAL cc_start: 0.8638 (t) cc_final: 0.8323 (p) REVERT: Q 957 THR cc_start: 0.7772 (p) cc_final: 0.7487 (t) REVERT: Q 1021 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7540 (m-30) REVERT: Q 1073 LEU cc_start: 0.8914 (tp) cc_final: 0.8649 (tt) REVERT: Q 1097 ASN cc_start: 0.8414 (p0) cc_final: 0.8181 (p0) REVERT: Q 1103 ASP cc_start: 0.8666 (p0) cc_final: 0.7475 (p0) REVERT: Q 1139 GLU cc_start: 0.8167 (tp30) cc_final: 0.7929 (tp30) REVERT: Q 1160 LYS cc_start: 0.8228 (ptpp) cc_final: 0.7921 (ptpp) REVERT: Q 1204 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8391 (t0) REVERT: Q 1266 GLU cc_start: 0.7916 (mp0) cc_final: 0.7477 (mp0) REVERT: Q 1280 LYS cc_start: 0.8582 (ptpp) cc_final: 0.8317 (ptpp) REVERT: Q 1301 LEU cc_start: 0.8368 (tp) cc_final: 0.7960 (tt) REVERT: Q 1305 ASP cc_start: 0.8303 (m-30) cc_final: 0.7954 (m-30) REVERT: Q 1432 MET cc_start: 0.5843 (tpp) cc_final: 0.5561 (tpp) outliers start: 103 outliers final: 61 residues processed: 876 average time/residue: 1.5939 time to fit residues: 1605.1686 Evaluate side-chains 901 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 819 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 69 LYS Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 591 LEU Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 119 GLU Chi-restraints excluded: chain T residue 141 GLU Chi-restraints excluded: chain T residue 148 THR Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain T residue 318 ILE Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 136 ILE Chi-restraints excluded: chain U residue 170 GLU Chi-restraints excluded: chain U residue 239 VAL Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 350 ARG Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 188 SER Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain V residue 451 ARG Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 131 GLU Chi-restraints excluded: chain W residue 134 GLU Chi-restraints excluded: chain W residue 233 LYS Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 336 ASN Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 373 GLN Chi-restraints excluded: chain W residue 455 GLN Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 156 LEU 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 265 VAL Chi-restraints excluded: chain X residue 324 LEU Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 238 THR Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 323 MET Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 361 GLU Chi-restraints excluded: chain Y residue 374 GLU Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 440 VAL Chi-restraints excluded: chain Q residue 1021 ASP Chi-restraints excluded: chain Q residue 1091 GLU Chi-restraints excluded: chain Q residue 1150 LYS Chi-restraints excluded: chain Q residue 1162 THR Chi-restraints excluded: chain Q residue 1203 LEU Chi-restraints excluded: chain Q residue 1204 ASN Chi-restraints excluded: chain Q residue 1343 ILE Chi-restraints excluded: chain Q residue 1361 TRP Chi-restraints excluded: chain Q residue 1405 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 2.9990 chunk 262 optimal weight: 0.9980 chunk 282 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 188 optimal weight: 0.5980 chunk 163 optimal weight: 0.7980 chunk 241 optimal weight: 2.9990 chunk 338 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 633 GLN S 141 GLN U 310 ASN V 256 ASN V 263 GLN ** V 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 394 GLN V 417 GLN W 173 ASN X 271 GLN X 289 ASN X 325 ASN Y 49 GLN ** Y 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.118642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.098404 restraints weight = 44186.059| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.26 r_work: 0.3170 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 29104 Z= 0.244 Angle : 0.677 9.784 39373 Z= 0.337 Chirality : 0.047 0.241 4620 Planarity : 0.007 0.411 5040 Dihedral : 7.005 122.053 4004 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.57 % Allowed : 29.29 % Favored : 67.13 % 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: 0.19 (0.14), residues: 3618 helix: 1.04 (0.14), residues: 1524 sheet: 0.52 (0.20), residues: 663 loop : -1.03 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Y 280 HIS 0.008 0.001 HIS V 165 PHE 0.029 0.002 PHE R 691 TYR 0.023 0.002 TYR X 295 ARG 0.008 0.001 ARG Q1078 Details of bonding type rmsd hydrogen bonds : bond 0.05150 ( 1072) hydrogen bonds : angle 4.09590 ( 3135) covalent geometry : bond 0.00590 (29102) covalent geometry : angle 0.67725 (39373) Misc. bond : bond 0.00531 ( 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 952 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 839 time to evaluate : 3.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.8595 (p0) cc_final: 0.8146 (p0) REVERT: R 38 SER cc_start: 0.8515 (t) cc_final: 0.8259 (m) REVERT: R 70 PHE cc_start: 0.7704 (t80) cc_final: 0.7390 (t80) REVERT: R 75 LEU cc_start: 0.8544 (mm) cc_final: 0.8137 (tm) REVERT: R 95 GLN cc_start: 0.8544 (mt0) cc_final: 0.8164 (mt0) REVERT: R 112 GLU cc_start: 0.7937 (tt0) cc_final: 0.7721 (tt0) REVERT: R 113 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: R 121 HIS cc_start: 0.8554 (OUTLIER) cc_final: 0.8155 (m-70) REVERT: R 146 GLN cc_start: 0.7780 (mm110) cc_final: 0.7500 (mm-40) REVERT: R 193 ASP cc_start: 0.7781 (p0) cc_final: 0.7527 (p0) REVERT: R 242 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7036 (mp10) REVERT: R 249 ASP cc_start: 0.8229 (m-30) cc_final: 0.7921 (m-30) REVERT: R 608 GLU cc_start: 0.8355 (tt0) cc_final: 0.7975 (mt-10) REVERT: R 609 GLN cc_start: 0.8095 (mt0) cc_final: 0.7768 (mt0) REVERT: R 614 LEU cc_start: 0.8018 (mt) cc_final: 0.7816 (mp) REVERT: R 623 GLU cc_start: 0.8529 (tp30) cc_final: 0.8057 (tm-30) REVERT: R 643 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8109 (tm-30) REVERT: R 719 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7295 (mpp80) REVERT: S 159 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7932 (ptm160) REVERT: T 90 LEU cc_start: 0.8726 (mm) cc_final: 0.8516 (mt) REVERT: T 119 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: T 187 GLU cc_start: 0.7602 (tp30) cc_final: 0.7400 (tp30) REVERT: T 203 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: T 205 ASN cc_start: 0.8448 (m-40) cc_final: 0.7833 (m-40) REVERT: T 330 SER cc_start: 0.8789 (m) cc_final: 0.8498 (t) REVERT: T 332 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7709 (tp) REVERT: T 355 SER cc_start: 0.8446 (t) cc_final: 0.8230 (p) REVERT: T 386 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8420 (mpt180) REVERT: T 392 ARG cc_start: 0.8237 (mtm110) cc_final: 0.7935 (mtm-85) REVERT: U 32 ASP cc_start: 0.7934 (m-30) cc_final: 0.7695 (m-30) REVERT: U 71 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8361 (t) REVERT: U 110 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7448 (pp20) REVERT: U 170 GLU cc_start: 0.8160 (tp30) cc_final: 0.7892 (tp30) REVERT: U 174 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7909 (mtpt) REVERT: U 193 ASP cc_start: 0.8360 (t0) cc_final: 0.8112 (t0) REVERT: U 233 LYS cc_start: 0.8335 (mmmt) cc_final: 0.8123 (mmmt) REVERT: U 255 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8477 (mp) REVERT: U 271 ASP cc_start: 0.8117 (m-30) cc_final: 0.7882 (m-30) REVERT: U 282 GLU cc_start: 0.8448 (tp30) cc_final: 0.8069 (tp30) REVERT: U 393 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: U 455 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7823 (mp10) REVERT: V 42 LYS cc_start: 0.8255 (mtmm) cc_final: 0.7772 (tttm) REVERT: V 135 GLU cc_start: 0.7539 (tt0) cc_final: 0.7299 (tt0) REVERT: V 148 THR cc_start: 0.8801 (m) cc_final: 0.8601 (p) REVERT: V 154 ASN cc_start: 0.8080 (t0) cc_final: 0.7738 (t0) REVERT: V 203 GLU cc_start: 0.8117 (tt0) cc_final: 0.7910 (tt0) REVERT: V 298 GLN cc_start: 0.8197 (mp10) cc_final: 0.7962 (mp10) REVERT: V 451 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.6941 (mtp180) REVERT: W 177 ASP cc_start: 0.8579 (m-30) cc_final: 0.8314 (m-30) REVERT: W 226 GLU cc_start: 0.7702 (mp0) cc_final: 0.7427 (mp0) REVERT: W 374 GLU cc_start: 0.7572 (tp30) cc_final: 0.7304 (tt0) REVERT: W 385 ASP cc_start: 0.8140 (m-30) cc_final: 0.7754 (m-30) REVERT: W 389 LYS cc_start: 0.8521 (tttp) cc_final: 0.7770 (mmmm) REVERT: W 393 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7268 (mp0) REVERT: W 419 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7503 (mp0) REVERT: W 425 ARG cc_start: 0.8641 (ttt90) cc_final: 0.8364 (ttt90) REVERT: X 37 GLU cc_start: 0.7888 (pp20) cc_final: 0.7590 (pp20) REVERT: X 94 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7683 (mp10) REVERT: X 135 GLU cc_start: 0.7626 (tt0) cc_final: 0.7311 (mt-10) REVERT: X 206 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8345 (t) REVERT: X 229 TYR cc_start: 0.8779 (m-80) cc_final: 0.8559 (m-80) REVERT: X 282 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7900 (tm-30) REVERT: X 341 ASN cc_start: 0.8856 (p0) cc_final: 0.8611 (p0) REVERT: X 390 VAL cc_start: 0.8562 (t) cc_final: 0.8283 (p) REVERT: X 396 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6926 (tm-30) REVERT: Y 81 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8283 (mtmm) REVERT: Y 106 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8347 (mp) REVERT: Y 115 GLU cc_start: 0.7801 (tp30) cc_final: 0.7544 (tp30) REVERT: Y 144 GLN cc_start: 0.7032 (mp10) cc_final: 0.6733 (mp10) REVERT: Y 202 LEU cc_start: 0.8989 (mm) cc_final: 0.8712 (mp) REVERT: Y 350 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7886 (mtp85) REVERT: Y 392 VAL cc_start: 0.8785 (t) cc_final: 0.8548 (t) REVERT: Y 404 SER cc_start: 0.8674 (t) cc_final: 0.8231 (m) REVERT: Q 957 THR cc_start: 0.7767 (p) cc_final: 0.7483 (t) REVERT: Q 1021 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: Q 1097 ASN cc_start: 0.8467 (p0) cc_final: 0.8240 (p0) REVERT: Q 1103 ASP cc_start: 0.8691 (p0) cc_final: 0.7887 (p0) REVERT: Q 1160 LYS cc_start: 0.8266 (ptpp) cc_final: 0.7986 (ptpp) REVERT: Q 1173 GLU cc_start: 0.7354 (pp20) cc_final: 0.6975 (pp20) REVERT: Q 1266 GLU cc_start: 0.7952 (mp0) cc_final: 0.7512 (mp0) REVERT: Q 1280 LYS cc_start: 0.8608 (ptpp) cc_final: 0.8338 (ptpp) REVERT: Q 1292 ASP cc_start: 0.7659 (m-30) cc_final: 0.7324 (m-30) REVERT: Q 1432 MET cc_start: 0.5830 (tpp) cc_final: 0.5556 (tpp) outliers start: 113 outliers final: 64 residues processed: 895 average time/residue: 1.6005 time to fit residues: 1639.7259 Evaluate side-chains 894 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 810 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 69 LYS Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 591 LEU Chi-restraints excluded: chain R residue 607 HIS Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 159 ARG Chi-restraints excluded: chain T residue 119 GLU Chi-restraints excluded: chain T residue 148 THR Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain T residue 318 ILE Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 114 THR Chi-restraints excluded: chain U residue 136 ILE Chi-restraints excluded: chain U residue 229 LEU Chi-restraints excluded: chain U residue 239 VAL Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 350 ARG Chi-restraints excluded: chain U residue 393 GLU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 455 GLN Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 188 SER Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 373 LEU Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 398 SER Chi-restraints excluded: chain V residue 451 ARG Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 131 GLU Chi-restraints excluded: chain W residue 134 GLU Chi-restraints excluded: chain W residue 233 LYS Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 156 LEU 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 265 VAL Chi-restraints excluded: chain X residue 324 LEU Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain Y residue 81 LYS Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 238 THR Chi-restraints excluded: chain Y residue 267 SER Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 323 MET Chi-restraints excluded: chain Y residue 335 THR Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 361 GLU Chi-restraints excluded: chain Y residue 374 GLU Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 440 VAL Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 1021 ASP Chi-restraints excluded: chain Q residue 1091 GLU Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1150 LYS Chi-restraints excluded: chain Q residue 1152 VAL Chi-restraints excluded: chain Q residue 1161 ASN Chi-restraints excluded: chain Q residue 1162 THR Chi-restraints excluded: chain Q residue 1203 LEU Chi-restraints excluded: chain Q residue 1361 TRP Chi-restraints excluded: chain Q residue 1405 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 317 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 309 optimal weight: 0.9980 chunk 319 optimal weight: 5.9990 chunk 191 optimal weight: 0.1980 chunk 143 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 chunk 195 optimal weight: 0.5980 chunk 335 optimal weight: 0.0870 chunk 209 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 633 GLN S 141 GLN U 310 ASN V 263 GLN V 394 GLN V 417 GLN W 173 ASN X 256 ASN X 271 GLN X 289 ASN X 325 ASN Y 49 GLN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.120942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.100400 restraints weight = 44064.382| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.13 r_work: 0.3211 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29104 Z= 0.132 Angle : 0.615 8.693 39373 Z= 0.303 Chirality : 0.043 0.241 4620 Planarity : 0.004 0.155 5040 Dihedral : 6.647 116.752 4004 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.75 % Allowed : 30.47 % Favored : 66.78 % 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: 0.37 (0.14), residues: 3618 helix: 1.22 (0.14), residues: 1523 sheet: 0.55 (0.20), residues: 653 loop : -0.92 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 280 HIS 0.007 0.001 HIS V 165 PHE 0.021 0.001 PHE R 691 TYR 0.046 0.001 TYR R 724 ARG 0.023 0.001 ARG X 180 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 1072) hydrogen bonds : angle 3.91564 ( 3135) covalent geometry : bond 0.00316 (29102) covalent geometry : angle 0.61537 (39373) Misc. bond : bond 0.00318 ( 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 898 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 811 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASN cc_start: 0.8587 (p0) cc_final: 0.8132 (p0) REVERT: R 38 SER cc_start: 0.8479 (t) cc_final: 0.8229 (m) REVERT: R 70 PHE cc_start: 0.7675 (t80) cc_final: 0.7347 (t80) REVERT: R 75 LEU cc_start: 0.8494 (mm) cc_final: 0.8093 (tm) REVERT: R 95 GLN cc_start: 0.8549 (mt0) cc_final: 0.8191 (mt0) REVERT: R 101 ASP cc_start: 0.7948 (t70) cc_final: 0.7481 (p0) REVERT: R 112 GLU cc_start: 0.7865 (tt0) cc_final: 0.7660 (tt0) REVERT: R 113 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: R 117 TYR cc_start: 0.8671 (t80) cc_final: 0.8237 (t80) REVERT: R 121 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.8121 (m-70) REVERT: R 146 GLN cc_start: 0.7703 (mm110) cc_final: 0.7412 (mm-40) REVERT: R 193 ASP cc_start: 0.7738 (p0) cc_final: 0.7473 (p0) REVERT: R 249 ASP cc_start: 0.8160 (m-30) cc_final: 0.7834 (m-30) REVERT: R 278 GLU cc_start: 0.7976 (tt0) cc_final: 0.7499 (tt0) REVERT: R 608 GLU cc_start: 0.8336 (tt0) cc_final: 0.7979 (mt-10) REVERT: R 609 GLN cc_start: 0.8095 (mt0) cc_final: 0.7773 (mt0) REVERT: R 623 GLU cc_start: 0.8534 (tp30) cc_final: 0.8094 (tm-30) REVERT: R 643 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8061 (tm-30) REVERT: R 719 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7180 (mpp80) REVERT: T 90 LEU cc_start: 0.8693 (mm) cc_final: 0.8481 (mt) REVERT: T 187 GLU cc_start: 0.7604 (tp30) cc_final: 0.7259 (tp30) REVERT: T 203 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: T 205 ASN cc_start: 0.8447 (m-40) cc_final: 0.8105 (m-40) REVERT: T 330 SER cc_start: 0.8707 (m) cc_final: 0.8414 (t) REVERT: T 332 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7740 (tp) REVERT: T 355 SER cc_start: 0.8361 (t) cc_final: 0.8132 (p) REVERT: T 386 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8377 (mpt180) REVERT: T 392 ARG cc_start: 0.8220 (mtm110) cc_final: 0.7925 (mtm-85) REVERT: T 454 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8270 (mttt) REVERT: U 32 ASP cc_start: 0.7951 (m-30) cc_final: 0.7628 (m-30) REVERT: U 71 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8420 (p) REVERT: U 110 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7421 (pp20) REVERT: U 170 GLU cc_start: 0.8163 (tp30) cc_final: 0.7902 (tp30) REVERT: U 174 LYS cc_start: 0.8051 (mtpt) cc_final: 0.7817 (mtpt) REVERT: U 233 LYS cc_start: 0.8333 (mmmt) cc_final: 0.8117 (mmmt) REVERT: U 255 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8468 (mp) REVERT: U 271 ASP cc_start: 0.8075 (m-30) cc_final: 0.7833 (m-30) REVERT: U 282 GLU cc_start: 0.8429 (tp30) cc_final: 0.8069 (tp30) REVERT: V 42 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7789 (tttm) REVERT: V 135 GLU cc_start: 0.7537 (tt0) cc_final: 0.7309 (tt0) REVERT: V 148 THR cc_start: 0.8855 (m) cc_final: 0.8629 (p) REVERT: V 154 ASN cc_start: 0.8039 (t0) cc_final: 0.7676 (t0) REVERT: V 168 VAL cc_start: 0.9016 (p) cc_final: 0.8732 (t) REVERT: V 180 ARG cc_start: 0.8801 (ttp80) cc_final: 0.8586 (ttp80) REVERT: V 385 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7937 (mm-30) REVERT: V 400 LEU cc_start: 0.8331 (tp) cc_final: 0.7890 (mt) REVERT: W 177 ASP cc_start: 0.8565 (m-30) cc_final: 0.8270 (m-30) REVERT: W 374 GLU cc_start: 0.7506 (tp30) cc_final: 0.7242 (tt0) REVERT: W 385 ASP cc_start: 0.8072 (m-30) cc_final: 0.7679 (m-30) REVERT: W 389 LYS cc_start: 0.8437 (tttp) cc_final: 0.7708 (ttpp) REVERT: W 393 GLU cc_start: 0.7346 (mt-10) cc_final: 0.6951 (mp0) REVERT: W 419 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7485 (mp0) REVERT: W 425 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8320 (ttt90) REVERT: X 37 GLU cc_start: 0.7886 (pp20) cc_final: 0.7588 (pp20) REVERT: X 94 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7535 (mp10) REVERT: X 135 GLU cc_start: 0.7591 (tt0) cc_final: 0.7282 (mt-10) REVERT: X 221 GLU cc_start: 0.7649 (tt0) cc_final: 0.7415 (tm-30) REVERT: X 229 TYR cc_start: 0.8755 (m-80) cc_final: 0.8534 (m-80) REVERT: X 282 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7838 (tm-30) REVERT: X 341 ASN cc_start: 0.8837 (p0) cc_final: 0.8579 (p0) REVERT: Y 81 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8237 (mtmm) REVERT: Y 106 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8343 (mp) REVERT: Y 115 GLU cc_start: 0.7700 (tp30) cc_final: 0.7423 (tp30) REVERT: Y 144 GLN cc_start: 0.7030 (mp10) cc_final: 0.6740 (mp10) REVERT: Y 193 ASP cc_start: 0.8263 (t70) cc_final: 0.8024 (t0) REVERT: Y 202 LEU cc_start: 0.8998 (mm) cc_final: 0.8714 (mp) REVERT: Y 285 LYS cc_start: 0.8600 (tttt) cc_final: 0.8303 (ttpt) REVERT: Y 350 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7873 (mtm-85) REVERT: Y 392 VAL cc_start: 0.8626 (t) cc_final: 0.8281 (p) REVERT: Q 957 THR cc_start: 0.7784 (p) cc_final: 0.7497 (t) REVERT: Q 1009 LYS cc_start: 0.8346 (mtmm) cc_final: 0.8051 (mtpp) REVERT: Q 1021 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7519 (m-30) REVERT: Q 1103 ASP cc_start: 0.8650 (p0) cc_final: 0.7453 (p0) REVERT: Q 1160 LYS cc_start: 0.8267 (ptpp) cc_final: 0.7987 (ptpp) REVERT: Q 1161 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7797 (m110) REVERT: Q 1173 GLU cc_start: 0.7345 (pp20) cc_final: 0.6997 (pp20) REVERT: Q 1266 GLU cc_start: 0.7903 (mp0) cc_final: 0.7463 (mp0) REVERT: Q 1280 LYS cc_start: 0.8582 (ptpp) cc_final: 0.8301 (ptpp) REVERT: Q 1292 ASP cc_start: 0.7616 (m-30) cc_final: 0.7256 (m-30) REVERT: Q 1301 LEU cc_start: 0.8406 (tt) cc_final: 0.8079 (tp) REVERT: Q 1305 ASP cc_start: 0.8274 (m-30) cc_final: 0.7996 (m-30) REVERT: Q 1432 MET cc_start: 0.5754 (tpp) cc_final: 0.5461 (tpp) outliers start: 87 outliers final: 56 residues processed: 852 average time/residue: 1.6600 time to fit residues: 1613.9414 Evaluate side-chains 868 residues out of total 3167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 797 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 69 LYS Chi-restraints excluded: chain R residue 113 GLU Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain T residue 148 THR Chi-restraints excluded: chain T residue 203 GLU Chi-restraints excluded: chain T residue 318 ILE Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 367 LEU Chi-restraints excluded: chain T residue 386 ARG Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 114 THR Chi-restraints excluded: chain U residue 136 ILE Chi-restraints excluded: chain U residue 239 VAL Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 350 ARG Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 188 SER Chi-restraints excluded: chain V residue 319 GLU Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 398 SER Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 131 GLU Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 327 ARG Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 425 ARG Chi-restraints excluded: chain W residue 455 GLN Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 94 GLN Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 156 LEU 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 265 VAL Chi-restraints excluded: chain X residue 324 LEU Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain Y residue 81 LYS Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 183 LYS Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 238 THR Chi-restraints excluded: chain Y residue 267 SER Chi-restraints excluded: chain Y residue 269 VAL Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 323 MET Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 361 GLU Chi-restraints excluded: chain Y residue 374 GLU Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain Y residue 440 VAL Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 983 THR Chi-restraints excluded: chain Q residue 1021 ASP Chi-restraints excluded: chain Q residue 1091 GLU Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1161 ASN Chi-restraints excluded: chain Q residue 1162 THR Chi-restraints excluded: chain Q residue 1203 LEU Chi-restraints excluded: chain Q residue 1361 TRP Chi-restraints excluded: chain Q residue 1405 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 200 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 69 optimal weight: 0.0270 chunk 110 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 56 HIS R 633 GLN S 141 GLN V 263 GLN V 394 GLN V 417 GLN W 173 ASN X 271 GLN X 289 ASN X 314 ASN X 325 ASN Y 49 GLN Q1244 GLN ** Q1279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.120682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.099937 restraints weight = 44149.984| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.15 r_work: 0.3202 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29104 Z= 0.154 Angle : 0.627 10.172 39373 Z= 0.309 Chirality : 0.044 0.244 4620 Planarity : 0.007 0.447 5040 Dihedral : 6.854 117.427 4004 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.91 % Allowed : 30.40 % Favored : 66.69 % 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: 0.39 (0.14), residues: 3618 helix: 1.23 (0.14), residues: 1523 sheet: 0.53 (0.20), residues: 655 loop : -0.90 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Y 280 HIS 0.005 0.001 HIS R 745 PHE 0.022 0.001 PHE R 691 TYR 0.041 0.002 TYR R 724 ARG 0.012 0.000 ARG T 431 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 1072) hydrogen bonds : angle 3.91858 ( 3135) covalent geometry : bond 0.00372 (29102) covalent geometry : angle 0.62736 (39373) Misc. bond : bond 0.00266 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31042.21 seconds wall clock time: 532 minutes 39.28 seconds (31959.28 seconds total)