Starting phenix.real_space_refine on Mon Sep 14 00:10:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23cp_68865/09_2026/23cp_68865.cif Found real_map, /net/cci-nas-00/data/ceres_data/23cp_68865/09_2026/23cp_68865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/23cp_68865/09_2026/23cp_68865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23cp_68865/09_2026/23cp_68865.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/23cp_68865/09_2026/23cp_68865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23cp_68865/09_2026/23cp_68865.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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 Zn 3 6.06 5 S 111 5.16 5 C 16353 2.51 5 N 4634 2.21 5 O 4877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25978 Number of models: 1 Model: "" Number of chains: 13 Chain: "K" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1321 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 157} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "N" Number of atoms: 3758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3758 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 450} Chain breaks: 3 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "O" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2890 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 336} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3064 Classifications: {'peptide': 376} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 21, 'TRANS': 354} Chain breaks: 6 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Q" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2750 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 313} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "R" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3289 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 390} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3184 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 365} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1514 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 173} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3070 Classifications: {'peptide': 407} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 14} Link IDs: {'PTRANS': 31, 'TRANS': 375} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 1, 'TYR:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "U" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1135 Classifications: {'peptide': 150} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 144} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 57 Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2901 SG CYS N 320 60.256 151.091 88.362 1.00132.27 S ATOM 2927 SG CYS N 323 57.472 153.316 90.037 1.00109.70 S ATOM 3122 SG CYS N 348 59.877 154.485 87.157 1.00129.02 S ATOM 3141 SG CYS N 351 60.918 154.027 90.818 1.00140.32 S ATOM 6263 SG CYS O 320 82.588 187.674 92.118 1.00149.98 S ATOM 6289 SG CYS O 323 80.154 185.272 91.057 1.00161.64 S ATOM 6490 SG CYS O 348 81.180 188.123 88.637 1.00189.08 S ATOM 6509 SG CYS O 351 79.029 189.029 91.524 1.00170.92 S ATOM 19825 SG CYS S 547 59.536 64.337 63.514 1.00108.16 S ATOM 19847 SG CYS S 550 59.483 68.040 63.230 1.00112.20 S ATOM 20012 SG CYS S 571 57.013 65.955 61.165 1.00103.37 S ATOM 20034 SG CYS S 574 60.589 65.980 60.159 1.00 98.53 S Time building chain proxies: 5.60, per 1000 atoms: 0.22 Number of scatterers: 25978 At special positions: 0 Unit cell: (186.84, 234.36, 128.52, 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) Zn 3 29.99 S 111 16.00 O 4877 8.00 N 4634 7.00 C 16353 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN N 701 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 351 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 348 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 320 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 323 " pdb=" ZN O 701 " pdb="ZN ZN O 701 " - pdb=" SG CYS O 320 " pdb="ZN ZN O 701 " - pdb=" SG CYS O 348 " pdb="ZN ZN O 701 " - pdb=" SG CYS O 323 " pdb="ZN ZN O 701 " - pdb=" SG CYS O 351 " pdb=" ZN S 701 " pdb="ZN ZN S 701 " - pdb=" SG CYS S 571 " pdb="ZN ZN S 701 " - pdb=" SG CYS S 547 " pdb="ZN ZN S 701 " - pdb=" SG CYS S 550 " pdb="ZN ZN S 701 " - pdb=" SG CYS S 574 " Number of angles added : 18 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6242 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 20 sheets defined 50.3% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'K' and resid 172 through 191 removed outlier: 3.864A pdb=" N LYS K 191 " --> pdb=" O ARG K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 209 removed outlier: 3.802A pdb=" N ARG K 209 " --> pdb=" O GLU K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 335 removed outlier: 4.322A pdb=" N ALA K 315 " --> pdb=" O GLU K 311 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU K 335 " --> pdb=" O GLU K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 354 through 384 removed outlier: 3.901A pdb=" N LEU K 366 " --> pdb=" O GLU K 362 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR K 369 " --> pdb=" O LYS K 365 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER K 370 " --> pdb=" O LEU K 366 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS K 371 " --> pdb=" O ALA K 367 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG K 373 " --> pdb=" O TYR K 369 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA K 374 " --> pdb=" O SER K 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 387 No H-bonds generated for 'chain 'K' and resid 385 through 387' Processing helix chain 'K' and resid 408 through 418 removed outlier: 4.128A pdb=" N THR K 412 " --> pdb=" O GLU K 408 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 110 Processing helix chain 'N' and resid 122 through 124 No H-bonds generated for 'chain 'N' and resid 122 through 124' Processing helix chain 'N' and resid 132 through 139 Processing helix chain 'N' and resid 151 through 169 removed outlier: 3.920A pdb=" N ASN N 169 " --> pdb=" O ALA N 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 181 removed outlier: 3.745A pdb=" N CYS N 179 " --> pdb=" O THR N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 200 removed outlier: 3.583A pdb=" N ILE N 190 " --> pdb=" O ASP N 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 259 Processing helix chain 'N' and resid 348 through 353 Processing helix chain 'N' and resid 385 through 400 Processing helix chain 'N' and resid 402 through 411 removed outlier: 3.657A pdb=" N ILE N 406 " --> pdb=" O ASP N 402 " (cutoff:3.500A) Processing helix chain 'N' and resid 414 through 425 Processing helix chain 'N' and resid 430 through 434 Processing helix chain 'N' and resid 466 through 474 Processing helix chain 'N' and resid 535 through 565 Proline residue: N 543 - end of helix Proline residue: N 550 - end of helix Processing helix chain 'N' and resid 567 through 633 removed outlier: 3.686A pdb=" N ALA N 575 " --> pdb=" O ARG N 571 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS N 589 " --> pdb=" O GLU N 585 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TYR N 590 " --> pdb=" O LEU N 586 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE N 591 " --> pdb=" O LYS N 587 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE N 613 " --> pdb=" O ARG N 609 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU N 614 " --> pdb=" O GLN N 610 " (cutoff:3.500A) Processing helix chain 'N' and resid 640 through 650 removed outlier: 4.204A pdb=" N MET N 644 " --> pdb=" O GLN N 640 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA N 650 " --> pdb=" O GLN N 646 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 112 Processing helix chain 'O' and resid 132 through 139 Processing helix chain 'O' and resid 140 through 143 Processing helix chain 'O' and resid 151 through 168 Processing helix chain 'O' and resid 175 through 182 removed outlier: 3.794A pdb=" N CYS O 179 " --> pdb=" O THR O 175 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN O 182 " --> pdb=" O ALA O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 200 removed outlier: 3.508A pdb=" N ILE O 190 " --> pdb=" O ASP O 186 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TRP O 200 " --> pdb=" O PHE O 196 " (cutoff:3.500A) Processing helix chain 'O' and resid 349 through 355 removed outlier: 4.228A pdb=" N LEU O 353 " --> pdb=" O SER O 349 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU O 354 " --> pdb=" O THR O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 385 through 399 removed outlier: 3.808A pdb=" N GLU O 397 " --> pdb=" O LEU O 393 " (cutoff:3.500A) Processing helix chain 'O' and resid 402 through 411 removed outlier: 4.222A pdb=" N ILE O 406 " --> pdb=" O ASP O 402 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 425 Processing helix chain 'O' and resid 431 through 437 Processing helix chain 'O' and resid 464 through 480 removed outlier: 4.085A pdb=" N ASP O 474 " --> pdb=" O ALA O 470 " (cutoff:3.500A) Proline residue: O 475 - end of helix Processing helix chain 'O' and resid 563 through 584 removed outlier: 3.579A pdb=" N ARG O 567 " --> pdb=" O SER O 563 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU O 584 " --> pdb=" O MET O 580 " (cutoff:3.500A) Processing helix chain 'O' and resid 584 through 634 Processing helix chain 'P' and resid 62 through 69 removed outlier: 3.758A pdb=" N LYS P 66 " --> pdb=" O ASN P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 118 removed outlier: 4.311A pdb=" N ASP P 118 " --> pdb=" O LEU P 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 224 removed outlier: 4.186A pdb=" N PHE P 223 " --> pdb=" O ARG P 219 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE P 224 " --> pdb=" O PHE P 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 219 through 224' Processing helix chain 'P' and resid 300 through 308 removed outlier: 4.123A pdb=" N ILE P 306 " --> pdb=" O GLU P 302 " (cutoff:3.500A) Processing helix chain 'P' and resid 313 through 328 removed outlier: 3.718A pdb=" N ASN P 328 " --> pdb=" O TYR P 324 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 357 No H-bonds generated for 'chain 'P' and resid 355 through 357' Processing helix chain 'P' and resid 358 through 364 removed outlier: 3.602A pdb=" N LEU P 363 " --> pdb=" O LEU P 359 " (cutoff:3.500A) Processing helix chain 'P' and resid 382 through 388 removed outlier: 3.523A pdb=" N ASN P 388 " --> pdb=" O GLU P 384 " (cutoff:3.500A) Processing helix chain 'P' and resid 421 through 456 removed outlier: 3.694A pdb=" N LEU P 453 " --> pdb=" O LYS P 449 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER P 454 " --> pdb=" O HIS P 450 " (cutoff:3.500A) Processing helix chain 'P' and resid 459 through 480 removed outlier: 4.068A pdb=" N PHE P 463 " --> pdb=" O ASP P 459 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS P 465 " --> pdb=" O VAL P 461 " (cutoff:3.500A) Processing helix chain 'P' and resid 480 through 486 removed outlier: 3.940A pdb=" N GLY P 486 " --> pdb=" O ALA P 482 " (cutoff:3.500A) Processing helix chain 'P' and resid 516 through 519 Processing helix chain 'P' and resid 520 through 531 Processing helix chain 'Q' and resid 5 through 9 Processing helix chain 'Q' and resid 33 through 51 removed outlier: 3.731A pdb=" N VAL Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) Proline residue: Q 45 - end of helix removed outlier: 3.612A pdb=" N THR Q 51 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 78 removed outlier: 4.022A pdb=" N ARG Q 77 " --> pdb=" O PRO Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 163 through 167 Processing helix chain 'Q' and resid 170 through 187 Processing helix chain 'Q' and resid 302 through 323 removed outlier: 3.578A pdb=" N ARG Q 306 " --> pdb=" O LEU Q 302 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER Q 320 " --> pdb=" O GLU Q 316 " (cutoff:3.500A) Proline residue: Q 321 - end of helix Processing helix chain 'Q' and resid 373 through 417 removed outlier: 3.805A pdb=" N GLU Q 381 " --> pdb=" O ARG Q 377 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU Q 382 " --> pdb=" O LYS Q 378 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG Q 383 " --> pdb=" O ARG Q 379 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN Q 384 " --> pdb=" O VAL Q 380 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE Q 411 " --> pdb=" O ARG Q 407 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS Q 412 " --> pdb=" O SER Q 408 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU Q 417 " --> pdb=" O GLN Q 413 " (cutoff:3.500A) Processing helix chain 'Q' and resid 452 through 464 removed outlier: 3.835A pdb=" N LEU Q 462 " --> pdb=" O ARG Q 458 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL Q 463 " --> pdb=" O VAL Q 459 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 336 Processing helix chain 'R' and resid 338 through 355 removed outlier: 3.729A pdb=" N LYS R 351 " --> pdb=" O ASN R 347 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU R 355 " --> pdb=" O LYS R 351 " (cutoff:3.500A) Processing helix chain 'R' and resid 367 through 378 Processing helix chain 'R' and resid 378 through 384 Processing helix chain 'R' and resid 393 through 397 Processing helix chain 'R' and resid 412 through 420 Processing helix chain 'R' and resid 433 through 455 removed outlier: 3.552A pdb=" N MET R 453 " --> pdb=" O THR R 449 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL R 454 " --> pdb=" O ILE R 450 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N MET R 455 " --> pdb=" O ARG R 451 " (cutoff:3.500A) Processing helix chain 'R' and resid 456 through 464 Processing helix chain 'R' and resid 466 through 478 removed outlier: 4.275A pdb=" N LYS R 470 " --> pdb=" O TYR R 466 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP R 471 " --> pdb=" O PRO R 467 " (cutoff:3.500A) Processing helix chain 'R' and resid 485 through 500 Processing helix chain 'R' and resid 509 through 522 removed outlier: 3.543A pdb=" N PHE R 513 " --> pdb=" O ASP R 509 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU R 519 " --> pdb=" O MET R 515 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU R 520 " --> pdb=" O MET R 516 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG R 521 " --> pdb=" O ARG R 517 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER R 522 " --> pdb=" O THR R 518 " (cutoff:3.500A) Processing helix chain 'R' and resid 524 through 536 Processing helix chain 'R' and resid 551 through 555 Processing helix chain 'R' and resid 557 through 566 removed outlier: 3.523A pdb=" N LYS R 561 " --> pdb=" O ASN R 557 " (cutoff:3.500A) Processing helix chain 'R' and resid 570 through 585 Processing helix chain 'R' and resid 587 through 598 Processing helix chain 'R' and resid 599 through 611 removed outlier: 4.073A pdb=" N VAL R 603 " --> pdb=" O ASN R 599 " (cutoff:3.500A) Processing helix chain 'R' and resid 914 through 930 Processing helix chain 'R' and resid 933 through 950 removed outlier: 3.878A pdb=" N GLY R 950 " --> pdb=" O ALA R 946 " (cutoff:3.500A) Processing helix chain 'R' and resid 976 through 984 Processing helix chain 'R' and resid 986 through 997 Processing helix chain 'R' and resid 1000 through 1013 Processing helix chain 'S' and resid 14 through 22 removed outlier: 3.693A pdb=" N ARG S 18 " --> pdb=" O SER S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 128 Processing helix chain 'S' and resid 161 through 165 Processing helix chain 'S' and resid 190 through 202 Processing helix chain 'S' and resid 206 through 230 removed outlier: 4.737A pdb=" N GLY S 227 " --> pdb=" O GLU S 223 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL S 228 " --> pdb=" O GLU S 224 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU S 230 " --> pdb=" O ALA S 226 " (cutoff:3.500A) Processing helix chain 'S' and resid 309 through 311 No H-bonds generated for 'chain 'S' and resid 309 through 311' Processing helix chain 'S' and resid 340 through 354 removed outlier: 3.531A pdb=" N ILE S 344 " --> pdb=" O GLY S 340 " (cutoff:3.500A) Processing helix chain 'S' and resid 358 through 380 removed outlier: 4.123A pdb=" N ALA S 362 " --> pdb=" O GLU S 358 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR S 364 " --> pdb=" O VAL S 360 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU S 377 " --> pdb=" O LYS S 373 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA S 378 " --> pdb=" O LEU S 374 " (cutoff:3.500A) Processing helix chain 'S' and resid 427 through 431 removed outlier: 3.567A pdb=" N GLU S 431 " --> pdb=" O GLU S 428 " (cutoff:3.500A) Processing helix chain 'S' and resid 438 through 440 No H-bonds generated for 'chain 'S' and resid 438 through 440' Processing helix chain 'S' and resid 441 through 462 removed outlier: 3.659A pdb=" N ARG S 462 " --> pdb=" O ARG S 458 " (cutoff:3.500A) Processing helix chain 'S' and resid 553 through 557 removed outlier: 3.811A pdb=" N SER S 556 " --> pdb=" O TRP S 553 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL S 557 " --> pdb=" O GLY S 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 553 through 557' Processing helix chain 'S' and resid 571 through 582 Processing helix chain 'T' and resid 345 through 368 removed outlier: 3.630A pdb=" N GLU T 349 " --> pdb=" O ASN T 345 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL T 364 " --> pdb=" O VAL T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 385 through 387 No H-bonds generated for 'chain 'T' and resid 385 through 387' Processing helix chain 'T' and resid 415 through 422 removed outlier: 3.855A pdb=" N SER T 419 " --> pdb=" O LYS T 415 " (cutoff:3.500A) Processing helix chain 'T' and resid 437 through 443 Processing helix chain 'T' and resid 448 through 458 Processing helix chain 'T' and resid 473 through 478 Processing helix chain 'T' and resid 479 through 500 removed outlier: 4.450A pdb=" N ALA T 484 " --> pdb=" O PRO T 480 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA T 485 " --> pdb=" O GLU T 481 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TRP T 500 " --> pdb=" O TRP T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 502 through 507 Processing helix chain 'V' and resid 65 through 83 Proline residue: V 70 - end of helix Processing helix chain 'V' and resid 118 through 126 Processing helix chain 'V' and resid 130 through 153 removed outlier: 3.699A pdb=" N PHE V 134 " --> pdb=" O ASN V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 157 through 178 Processing helix chain 'V' and resid 233 through 237 Processing helix chain 'V' and resid 321 through 325 removed outlier: 4.353A pdb=" N ASN V 324 " --> pdb=" O ASP V 321 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA V 325 " --> pdb=" O TYR V 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 321 through 325' Processing helix chain 'V' and resid 349 through 365 removed outlier: 4.254A pdb=" N GLU V 356 " --> pdb=" O LEU V 352 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU V 357 " --> pdb=" O GLU V 353 " (cutoff:3.500A) Processing helix chain 'V' and resid 380 through 392 Processing helix chain 'V' and resid 392 through 405 Processing helix chain 'V' and resid 453 through 485 Processing helix chain 'V' and resid 513 through 531 removed outlier: 4.096A pdb=" N MET V 517 " --> pdb=" O SER V 513 " (cutoff:3.500A) Processing helix chain 'V' and resid 570 through 583 Processing helix chain 'U' and resid 852 through 856 Processing helix chain 'U' and resid 857 through 862 Processing helix chain 'U' and resid 895 through 941 removed outlier: 4.152A pdb=" N ARG U 899 " --> pdb=" O GLY U 895 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU U 901 " --> pdb=" O SER U 897 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA U 902 " --> pdb=" O VAL U 898 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN U 936 " --> pdb=" O GLU U 932 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG U 937 " --> pdb=" O ALA U 933 " (cutoff:3.500A) Processing helix chain 'U' and resid 946 through 983 removed outlier: 4.077A pdb=" N ARG U 974 " --> pdb=" O ALA U 970 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 341 through 342 Processing sheet with id=AA2, first strand: chain 'N' and resid 117 through 120 removed outlier: 6.165A pdb=" N ILE N 117 " --> pdb=" O ILE O 227 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASP O 229 " --> pdb=" O ILE N 117 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU N 119 " --> pdb=" O ASP O 229 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 273 through 277 removed outlier: 4.280A pdb=" N GLY N 273 " --> pdb=" O THR T 427 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 346 through 347 Processing sheet with id=AA5, first strand: chain 'O' and resid 216 through 217 Processing sheet with id=AA6, first strand: chain 'O' and resid 331 through 333 Processing sheet with id=AA7, first strand: chain 'P' and resid 271 through 277 removed outlier: 3.772A pdb=" N ARG P 126 " --> pdb=" O VAL P 400 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL Q 473 " --> pdb=" O ASP P 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 250 through 251 removed outlier: 3.842A pdb=" N ILE P 373 " --> pdb=" O LEU P 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 298 through 299 Processing sheet with id=AB1, first strand: chain 'Q' and resid 19 through 22 Processing sheet with id=AB2, first strand: chain 'Q' and resid 67 through 71 removed outlier: 6.485A pdb=" N LEU Q 148 " --> pdb=" O LEU Q 130 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU Q 130 " --> pdb=" O LEU Q 148 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU Q 103 " --> pdb=" O MET Q 99 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET Q 99 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 87 through 88 removed outlier: 3.639A pdb=" N ILE Q 87 " --> pdb=" O TYR Q 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 389 through 391 Processing sheet with id=AB5, first strand: chain 'R' and resid 621 through 623 removed outlier: 3.570A pdb=" N ILE R 622 " --> pdb=" O ILE R 890 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 899 through 900 Processing sheet with id=AB7, first strand: chain 'S' and resid 27 through 29 Processing sheet with id=AB8, first strand: chain 'S' and resid 132 through 133 Processing sheet with id=AB9, first strand: chain 'S' and resid 313 through 321 removed outlier: 3.660A pdb=" N VAL S 326 " --> pdb=" O GLU S 435 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU S 435 " --> pdb=" O VAL S 326 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'V' and resid 216 through 219 Processing sheet with id=AC2, first strand: chain 'V' and resid 318 through 319 1209 hydrogen bonds defined for protein. 3492 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: 4.58 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4455 1.32 - 1.44: 6810 1.44 - 1.57: 15061 1.57 - 1.70: 1 1.70 - 1.82: 189 Bond restraints: 26516 Sorted by residual: bond pdb=" C PHE Q 109 " pdb=" N GLN Q 110 " ideal model delta sigma weight residual 1.329 1.449 -0.120 1.43e-02 4.89e+03 7.05e+01 bond pdb=" C ALA P 451 " pdb=" N PHE P 452 " ideal model delta sigma weight residual 1.334 1.235 0.099 1.33e-02 5.65e+03 5.56e+01 bond pdb=" C TYR Q 108 " pdb=" N PHE Q 109 " ideal model delta sigma weight residual 1.330 1.439 -0.109 1.46e-02 4.69e+03 5.56e+01 bond pdb=" C PRO Q 321 " pdb=" N TYR Q 322 " ideal model delta sigma weight residual 1.333 1.421 -0.088 1.24e-02 6.50e+03 4.99e+01 bond pdb=" C PHE P 339 " pdb=" N ARG P 340 " ideal model delta sigma weight residual 1.330 1.240 0.090 1.30e-02 5.92e+03 4.82e+01 ... (remaining 26511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 35252 2.58 - 5.16: 548 5.16 - 7.74: 104 7.74 - 10.32: 19 10.32 - 12.89: 5 Bond angle restraints: 35928 Sorted by residual: angle pdb=" N PHE P 452 " pdb=" CA PHE P 452 " pdb=" C PHE P 452 " ideal model delta sigma weight residual 111.14 123.11 -11.97 1.08e+00 8.57e-01 1.23e+02 angle pdb=" C PHE Q 109 " pdb=" N GLN Q 110 " pdb=" CA GLN Q 110 " ideal model delta sigma weight residual 122.65 111.88 10.77 1.49e+00 4.50e-01 5.22e+01 angle pdb=" N PRO V 535 " pdb=" CA PRO V 535 " pdb=" C PRO V 535 " ideal model delta sigma weight residual 110.70 118.79 -8.09 1.22e+00 6.72e-01 4.39e+01 angle pdb=" N ARG N 567 " pdb=" CA ARG N 567 " pdb=" C ARG N 567 " ideal model delta sigma weight residual 114.56 106.85 7.71 1.27e+00 6.20e-01 3.68e+01 angle pdb=" C THR N 542 " pdb=" N PRO N 543 " pdb=" CA PRO N 543 " ideal model delta sigma weight residual 119.24 113.03 6.21 1.04e+00 9.25e-01 3.56e+01 ... (remaining 35923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 14034 17.92 - 35.84: 1699 35.84 - 53.75: 422 53.75 - 71.67: 76 71.67 - 89.59: 25 Dihedral angle restraints: 16256 sinusoidal: 6685 harmonic: 9571 Sorted by residual: dihedral pdb=" C TYR V 520 " pdb=" N TYR V 520 " pdb=" CA TYR V 520 " pdb=" CB TYR V 520 " ideal model delta harmonic sigma weight residual -122.60 -138.63 16.03 0 2.50e+00 1.60e-01 4.11e+01 dihedral pdb=" N TYR V 520 " pdb=" C TYR V 520 " pdb=" CA TYR V 520 " pdb=" CB TYR V 520 " ideal model delta harmonic sigma weight residual 122.80 137.61 -14.81 0 2.50e+00 1.60e-01 3.51e+01 dihedral pdb=" N THR N 542 " pdb=" C THR N 542 " pdb=" CA THR N 542 " pdb=" CB THR N 542 " ideal model delta harmonic sigma weight residual 123.40 138.11 -14.71 0 2.50e+00 1.60e-01 3.46e+01 ... (remaining 16253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 3904 0.134 - 0.267: 39 0.267 - 0.401: 3 0.401 - 0.535: 0 0.535 - 0.668: 2 Chirality restraints: 3948 Sorted by residual: chirality pdb=" CA THR N 542 " pdb=" N THR N 542 " pdb=" C THR N 542 " pdb=" CB THR N 542 " both_signs ideal model delta sigma weight residual False 2.53 1.86 0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" CA TYR V 520 " pdb=" N TYR V 520 " pdb=" C TYR V 520 " pdb=" CB TYR V 520 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CG LEU N 605 " pdb=" CB LEU N 605 " pdb=" CD1 LEU N 605 " pdb=" CD2 LEU N 605 " both_signs ideal model delta sigma weight residual False -2.59 -2.88 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 3945 not shown) Planarity restraints: 4725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP P 143 " 0.026 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP P 143 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP P 143 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP P 143 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP P 143 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP P 143 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP P 143 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 143 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 143 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP P 143 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU V 534 " -0.059 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO V 535 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO V 535 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO V 535 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP S 419 " -0.023 2.00e-02 2.50e+03 1.87e-02 8.74e+00 pdb=" CG TRP S 419 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP S 419 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP S 419 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP S 419 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP S 419 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP S 419 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 419 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 419 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP S 419 " -0.004 2.00e-02 2.50e+03 ... (remaining 4722 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 307 2.64 - 3.20: 24245 3.20 - 3.77: 40757 3.77 - 4.33: 52055 4.33 - 4.90: 83393 Nonbonded interactions: 200757 Sorted by model distance: nonbonded pdb=" O ARG R 998 " pdb=" NH1 ARG R 998 " model vdw 2.072 3.120 nonbonded pdb=" N GLU O 565 " pdb=" OE1 GLU O 565 " model vdw 2.206 3.120 nonbonded pdb=" O ALA R 496 " pdb=" OG1 THR R 500 " model vdw 2.212 3.040 nonbonded pdb=" CE1 PHE N 642 " pdb=" O LEU O 630 " model vdw 2.226 3.340 nonbonded pdb=" OG1 THR V 200 " pdb=" O LEU V 247 " model vdw 2.237 3.040 ... (remaining 200752 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 26.500 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 26528 Z= 0.262 Angle : 0.785 12.895 35946 Z= 0.437 Chirality : 0.048 0.668 3948 Planarity : 0.006 0.089 4725 Dihedral : 16.614 89.588 10014 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.36 % Allowed : 26.03 % Favored : 73.61 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3185 helix: 1.59 (0.14), residues: 1427 sheet: -0.02 (0.37), residues: 203 loop : -1.31 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG U 924 TYR 0.030 0.001 TYR O 399 PHE 0.046 0.002 PHE Q 128 TRP 0.062 0.002 TRP P 143 HIS 0.007 0.001 HIS P 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.26 (26516) covalent geometry : angle 0.77834 / 0.44 (35928) hydrogen bonds : bond 0.13699 / 9.29 ( 1209) hydrogen bonds : angle 5.64814 / 4.07 ( 3492) metal coordination : bond 0.00446 / 0.22 ( 12) metal coordination : angle 4.67908 / 2.77 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 751 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 331 TYR cc_start: 0.8092 (p90) cc_final: 0.7349 (p90) REVERT: N 565 GLU cc_start: 0.6601 (mm-30) cc_final: 0.5679 (mm-30) REVERT: N 606 GLU cc_start: 0.7944 (tp30) cc_final: 0.7714 (tp30) REVERT: N 623 VAL cc_start: 0.8718 (p) cc_final: 0.8429 (p) REVERT: P 224 PHE cc_start: 0.8316 (m-80) cc_final: 0.8096 (m-80) REVERT: P 305 GLU cc_start: 0.8537 (tp30) cc_final: 0.8230 (mm-30) REVERT: P 308 ASP cc_start: 0.8887 (t0) cc_final: 0.8582 (t0) REVERT: Q 136 GLN cc_start: 0.7664 (mt0) cc_final: 0.7341 (mt0) REVERT: Q 157 GLU cc_start: 0.8023 (mp0) cc_final: 0.7693 (mp0) REVERT: Q 181 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8346 (mm-40) REVERT: Q 194 PHE cc_start: 0.7287 (p90) cc_final: 0.6860 (p90) REVERT: Q 397 LYS cc_start: 0.8682 (tppt) cc_final: 0.8414 (tppt) REVERT: R 388 MET cc_start: 0.8622 (mtp) cc_final: 0.8366 (mmm) REVERT: R 411 ASP cc_start: 0.8267 (p0) cc_final: 0.8005 (p0) REVERT: T 420 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8386 (mtm110) REVERT: V 173 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8161 (mm-30) REVERT: V 176 ARG cc_start: 0.8295 (mtm110) cc_final: 0.7976 (mtm110) REVERT: V 471 MET cc_start: 0.8648 (tpt) cc_final: 0.8395 (tpt) REVERT: U 911 ARG cc_start: 0.8040 (mmt-90) cc_final: 0.7429 (mmt180) outliers start: 10 outliers final: 3 residues processed: 752 average time/residue: 0.2245 time to fit residues: 245.4965 Evaluate side-chains 708 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 705 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 366 LEU Chi-restraints excluded: chain R residue 435 GLU Chi-restraints excluded: chain S residue 583 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 ASN N 627 GLN ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 358 HIS P 419 ASN ** Q 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN Q 147 ASN R 907 ASN V 511 GLN ** U 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 906 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.134746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.110826 restraints weight = 59064.985| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.62 r_work: 0.3421 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26528 Z= 0.150 Angle : 0.647 11.147 35946 Z= 0.327 Chirality : 0.042 0.187 3948 Planarity : 0.005 0.074 4725 Dihedral : 4.417 31.365 3586 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.37 % Allowed : 24.22 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3185 helix: 1.85 (0.14), residues: 1441 sheet: 0.10 (0.38), residues: 188 loop : -1.30 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 998 TYR 0.021 0.001 TYR P 394 PHE 0.030 0.002 PHE V 75 TRP 0.032 0.001 TRP P 143 HIS 0.008 0.001 HIS U 896 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (26516) covalent geometry : angle 0.63503 / 0.33 (35928) hydrogen bonds : bond 0.05088 / 3.48 ( 1209) hydrogen bonds : angle 4.59186 / 3.30 ( 3492) metal coordination : bond 0.00535 / 0.26 ( 12) metal coordination : angle 5.52361 / 3.16 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 743 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 317 ARG cc_start: 0.9190 (mmm-85) cc_final: 0.8873 (tpp80) REVERT: N 221 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8597 (m) REVERT: N 331 TYR cc_start: 0.8575 (p90) cc_final: 0.7844 (p90) REVERT: N 369 MET cc_start: 0.7759 (mtt) cc_final: 0.7437 (mpp) REVERT: N 569 MET cc_start: 0.7497 (mmp) cc_final: 0.7286 (mmt) REVERT: N 623 VAL cc_start: 0.8729 (p) cc_final: 0.8438 (p) REVERT: N 627 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8232 (tp40) REVERT: O 210 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7993 (t0) REVERT: O 391 ARG cc_start: 0.8523 (ttm170) cc_final: 0.8158 (ttm170) REVERT: O 405 GLN cc_start: 0.7850 (pm20) cc_final: 0.7411 (pm20) REVERT: O 582 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: O 630 LEU cc_start: 0.7668 (tp) cc_final: 0.7416 (tt) REVERT: P 305 GLU cc_start: 0.8669 (tp30) cc_final: 0.8076 (tp30) REVERT: P 428 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6505 (pm20) REVERT: Q 40 TRP cc_start: 0.8802 (m-10) cc_final: 0.8348 (m-90) REVERT: Q 115 ARG cc_start: 0.7295 (mmt90) cc_final: 0.6891 (mmt180) REVERT: Q 157 GLU cc_start: 0.8011 (mp0) cc_final: 0.7711 (mp0) REVERT: Q 181 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8445 (mm110) REVERT: Q 194 PHE cc_start: 0.7459 (p90) cc_final: 0.7022 (p90) REVERT: Q 374 ASP cc_start: 0.7555 (p0) cc_final: 0.7348 (p0) REVERT: Q 397 LYS cc_start: 0.8666 (tppt) cc_final: 0.8408 (tppt) REVERT: R 355 GLU cc_start: 0.8193 (pm20) cc_final: 0.7972 (pm20) REVERT: R 388 MET cc_start: 0.8809 (mtp) cc_final: 0.8437 (mmm) REVERT: R 428 GLN cc_start: 0.6420 (tp40) cc_final: 0.6028 (tp40) REVERT: R 429 ASP cc_start: 0.7911 (m-30) cc_final: 0.7696 (m-30) REVERT: R 482 MET cc_start: 0.7934 (mtt) cc_final: 0.7642 (mtt) REVERT: T 477 LEU cc_start: 0.9068 (mt) cc_final: 0.8828 (mp) REVERT: V 69 MET cc_start: 0.8691 (pmm) cc_final: 0.8474 (pmm) REVERT: V 173 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8198 (mm-30) REVERT: V 471 MET cc_start: 0.8769 (tpt) cc_final: 0.8543 (tpt) REVERT: U 911 ARG cc_start: 0.8274 (mmt-90) cc_final: 0.7991 (mmt-90) REVERT: U 913 ARG cc_start: 0.8299 (ptt90) cc_final: 0.8022 (ptt90) REVERT: U 983 LEU cc_start: 0.8669 (tt) cc_final: 0.8457 (tt) outliers start: 93 outliers final: 47 residues processed: 783 average time/residue: 0.2179 time to fit residues: 250.1834 Evaluate side-chains 773 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 721 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 198 GLN Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 366 LEU Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 546 LEU Chi-restraints excluded: chain N residue 563 SER Chi-restraints excluded: chain N residue 627 GLN Chi-restraints excluded: chain N residue 644 MET Chi-restraints excluded: chain O residue 210 ASP Chi-restraints excluded: chain O residue 348 CYS Chi-restraints excluded: chain O residue 474 ASP Chi-restraints excluded: chain O residue 580 MET Chi-restraints excluded: chain O residue 582 GLU Chi-restraints excluded: chain P residue 68 ARG Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 141 GLN Chi-restraints excluded: chain P residue 315 GLN Chi-restraints excluded: chain P residue 364 THR Chi-restraints excluded: chain P residue 428 GLU Chi-restraints excluded: chain P residue 531 LEU Chi-restraints excluded: chain Q residue 26 TYR Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 378 LYS Chi-restraints excluded: chain Q residue 394 MET Chi-restraints excluded: chain Q residue 470 VAL Chi-restraints excluded: chain R residue 398 CYS Chi-restraints excluded: chain R residue 515 MET Chi-restraints excluded: chain R residue 516 MET Chi-restraints excluded: chain R residue 518 THR Chi-restraints excluded: chain R residue 928 ARG Chi-restraints excluded: chain S residue 102 MET Chi-restraints excluded: chain S residue 336 LEU Chi-restraints excluded: chain S residue 436 THR Chi-restraints excluded: chain S residue 437 LEU Chi-restraints excluded: chain S residue 583 LYS Chi-restraints excluded: chain T residue 349 GLU Chi-restraints excluded: chain V residue 119 ILE Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 237 LEU Chi-restraints excluded: chain V residue 260 THR Chi-restraints excluded: chain V residue 267 PHE Chi-restraints excluded: chain V residue 276 LEU Chi-restraints excluded: chain V residue 552 VAL Chi-restraints excluded: chain U residue 869 ASN Chi-restraints excluded: chain U residue 876 THR Chi-restraints excluded: chain U residue 900 HIS Chi-restraints excluded: chain U residue 978 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 116 optimal weight: 1.9990 chunk 240 optimal weight: 9.9990 chunk 195 optimal weight: 0.0870 chunk 310 optimal weight: 8.9990 chunk 294 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 ASN N 627 GLN ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 GLN ** Q 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN Q 147 ASN V 316 GLN ** U 896 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.133585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.109654 restraints weight = 60005.371| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.65 r_work: 0.3400 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26528 Z= 0.136 Angle : 0.638 9.997 35946 Z= 0.319 Chirality : 0.042 0.262 3948 Planarity : 0.005 0.078 4725 Dihedral : 4.315 29.346 3583 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.44 % Allowed : 24.62 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.15), residues: 3185 helix: 1.85 (0.14), residues: 1445 sheet: 0.08 (0.39), residues: 188 loop : -1.29 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 998 TYR 0.022 0.001 TYR Q 322 PHE 0.031 0.002 PHE V 75 TRP 0.030 0.001 TRP S 419 HIS 0.006 0.001 HIS U 896 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (26516) covalent geometry : angle 0.62720 / 0.32 (35928) hydrogen bonds : bond 0.04716 / 3.23 ( 1209) hydrogen bonds : angle 4.46529 / 3.22 ( 3492) metal coordination : bond 0.00463 / 0.19 ( 12) metal coordination : angle 5.29503 / 2.99 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 752 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 192 ASN cc_start: 0.8238 (t0) cc_final: 0.8024 (t0) REVERT: N 221 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8541 (m) REVERT: N 331 TYR cc_start: 0.8433 (p90) cc_final: 0.7588 (p90) REVERT: N 369 MET cc_start: 0.7791 (mtt) cc_final: 0.6824 (mtt) REVERT: N 611 GLN cc_start: 0.8322 (tp40) cc_final: 0.8069 (tm-30) REVERT: N 623 VAL cc_start: 0.8771 (p) cc_final: 0.8532 (p) REVERT: O 391 ARG cc_start: 0.8444 (ttm170) cc_final: 0.8209 (ttt180) REVERT: O 401 GLU cc_start: 0.3067 (OUTLIER) cc_final: -0.0711 (pm20) REVERT: O 405 GLN cc_start: 0.7741 (pm20) cc_final: 0.7521 (mp10) REVERT: O 422 PHE cc_start: 0.9080 (t80) cc_final: 0.8785 (t80) REVERT: O 424 GLN cc_start: 0.8704 (tp-100) cc_final: 0.8158 (tm-30) REVERT: P 224 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7769 (m-80) REVERT: P 305 GLU cc_start: 0.8673 (tp30) cc_final: 0.8040 (tp30) REVERT: Q 115 ARG cc_start: 0.7310 (mmt90) cc_final: 0.6627 (mmt180) REVERT: Q 145 ASP cc_start: 0.7894 (t0) cc_final: 0.7568 (t0) REVERT: Q 157 GLU cc_start: 0.7987 (mp0) cc_final: 0.7687 (mp0) REVERT: Q 181 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8384 (mm110) REVERT: Q 194 PHE cc_start: 0.7549 (p90) cc_final: 0.7118 (p90) REVERT: Q 313 TRP cc_start: 0.6864 (t60) cc_final: 0.6221 (t60) REVERT: Q 397 LYS cc_start: 0.8681 (tppt) cc_final: 0.8374 (tppt) REVERT: R 355 GLU cc_start: 0.8088 (pm20) cc_final: 0.7816 (pm20) REVERT: R 388 MET cc_start: 0.8807 (mtp) cc_final: 0.8441 (mmm) REVERT: R 428 GLN cc_start: 0.6450 (tp40) cc_final: 0.6088 (tp40) REVERT: S 224 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7211 (tm-30) REVERT: T 473 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: T 477 LEU cc_start: 0.9073 (mt) cc_final: 0.8842 (mp) REVERT: V 150 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7589 (tp30) REVERT: V 173 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8274 (mm-30) REVERT: V 176 ARG cc_start: 0.8084 (mtm110) cc_final: 0.7855 (mtm110) REVERT: V 471 MET cc_start: 0.8706 (tpt) cc_final: 0.8468 (tpt) REVERT: U 911 ARG cc_start: 0.8242 (mmt-90) cc_final: 0.7993 (mmt-90) REVERT: U 913 ARG cc_start: 0.8176 (ptt90) cc_final: 0.7899 (ptt90) outliers start: 95 outliers final: 59 residues processed: 796 average time/residue: 0.2219 time to fit residues: 259.0407 Evaluate side-chains 781 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 717 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 296 ASN Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 325 MET Chi-restraints excluded: chain K residue 332 LEU Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 380 ARG Chi-restraints excluded: chain N residue 477 SER Chi-restraints excluded: chain N residue 563 SER Chi-restraints excluded: chain N residue 586 LEU Chi-restraints excluded: chain N residue 607 ARG Chi-restraints excluded: chain N residue 615 ASP Chi-restraints excluded: chain N residue 644 MET Chi-restraints excluded: chain O residue 134 ILE Chi-restraints excluded: chain O residue 348 CYS Chi-restraints excluded: chain O residue 401 GLU Chi-restraints excluded: chain O residue 474 ASP Chi-restraints excluded: chain P residue 68 ARG Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain P residue 172 LEU Chi-restraints excluded: chain P residue 224 PHE Chi-restraints excluded: chain P residue 282 VAL Chi-restraints excluded: chain P residue 313 THR Chi-restraints excluded: chain P residue 315 GLN Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 364 THR Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain P residue 531 LEU Chi-restraints excluded: chain Q residue 26 TYR Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 147 ASN Chi-restraints excluded: chain Q residue 182 HIS Chi-restraints excluded: chain Q residue 394 MET Chi-restraints excluded: chain Q residue 470 VAL Chi-restraints excluded: chain R residue 398 CYS Chi-restraints excluded: chain R residue 435 GLU Chi-restraints excluded: chain R residue 516 MET Chi-restraints excluded: chain R residue 907 ASN Chi-restraints excluded: chain R residue 928 ARG Chi-restraints excluded: chain S residue 102 MET Chi-restraints excluded: chain S residue 336 LEU Chi-restraints excluded: chain S residue 436 THR Chi-restraints excluded: chain S residue 437 LEU Chi-restraints excluded: chain S residue 583 LYS Chi-restraints excluded: chain T residue 349 GLU Chi-restraints excluded: chain T residue 418 ILE Chi-restraints excluded: chain T residue 473 GLU Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 150 GLU Chi-restraints excluded: chain V residue 260 THR Chi-restraints excluded: chain V residue 267 PHE Chi-restraints excluded: chain V residue 379 VAL Chi-restraints excluded: chain V residue 558 VAL Chi-restraints excluded: chain U residue 869 ASN Chi-restraints excluded: chain U residue 876 THR Chi-restraints excluded: chain U residue 978 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 294 optimal weight: 0.5980 chunk 211 optimal weight: 0.9990 chunk 223 optimal weight: 0.0020 chunk 16 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 213 optimal weight: 0.4980 chunk 221 optimal weight: 0.8980 chunk 166 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 GLN ** K 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 ASN N 424 GLN N 627 GLN ** Q 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 323 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.129668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.106875 restraints weight = 61732.542| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.61 r_work: 0.3394 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26528 Z= 0.138 Angle : 0.647 11.392 35946 Z= 0.321 Chirality : 0.042 0.242 3948 Planarity : 0.005 0.075 4725 Dihedral : 4.312 29.350 3581 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.69 % Allowed : 25.20 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 3185 helix: 1.83 (0.14), residues: 1451 sheet: -0.06 (0.37), residues: 198 loop : -1.31 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 998 TYR 0.019 0.001 TYR K 369 PHE 0.035 0.001 PHE V 75 TRP 0.018 0.001 TRP S 419 HIS 0.004 0.001 HIS R 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (26516) covalent geometry : angle 0.63451 / 0.32 (35928) hydrogen bonds : bond 0.04631 / 3.16 ( 1209) hydrogen bonds : angle 4.41775 / 3.19 ( 3492) metal coordination : bond 0.00547 / 0.20 ( 12) metal coordination : angle 5.68844 / 3.28 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 731 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 221 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8452 (m) REVERT: N 331 TYR cc_start: 0.8422 (p90) cc_final: 0.7855 (p90) REVERT: O 401 GLU cc_start: 0.3070 (OUTLIER) cc_final: -0.0872 (pm20) REVERT: O 414 THR cc_start: 0.8399 (p) cc_final: 0.8166 (p) REVERT: O 422 PHE cc_start: 0.9046 (t80) cc_final: 0.8812 (t80) REVERT: O 424 GLN cc_start: 0.8739 (tp-100) cc_final: 0.8302 (tm-30) REVERT: O 619 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8430 (t80) REVERT: P 224 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7829 (m-80) REVERT: P 230 GLU cc_start: 0.7111 (mp0) cc_final: 0.6805 (mp0) REVERT: P 305 GLU cc_start: 0.8693 (tp30) cc_final: 0.8049 (tp30) REVERT: P 453 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7695 (mm) REVERT: Q 115 ARG cc_start: 0.7286 (mmt90) cc_final: 0.6655 (mmt180) REVERT: Q 145 ASP cc_start: 0.7970 (t0) cc_final: 0.7629 (t0) REVERT: Q 157 GLU cc_start: 0.7997 (mp0) cc_final: 0.7699 (mp0) REVERT: Q 175 GLN cc_start: 0.8560 (pp30) cc_final: 0.8284 (pp30) REVERT: Q 181 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8358 (mm110) REVERT: Q 194 PHE cc_start: 0.7461 (p90) cc_final: 0.6957 (p90) REVERT: Q 313 TRP cc_start: 0.6793 (t60) cc_final: 0.6208 (t60) REVERT: Q 397 LYS cc_start: 0.8677 (tppt) cc_final: 0.8393 (tppt) REVERT: R 355 GLU cc_start: 0.8063 (pm20) cc_final: 0.7792 (pm20) REVERT: R 388 MET cc_start: 0.8854 (mtp) cc_final: 0.8518 (mmm) REVERT: S 224 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7295 (tm-30) REVERT: S 435 GLU cc_start: 0.8499 (pm20) cc_final: 0.8273 (pm20) REVERT: S 590 MET cc_start: 0.8783 (mmm) cc_final: 0.8559 (mmm) REVERT: T 473 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7838 (tm-30) REVERT: T 477 LEU cc_start: 0.9066 (mt) cc_final: 0.8705 (mp) REVERT: V 150 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7554 (tp30) REVERT: V 173 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8264 (mm-30) REVERT: V 176 ARG cc_start: 0.8147 (mtm110) cc_final: 0.7838 (mtm110) REVERT: V 471 MET cc_start: 0.8789 (tpt) cc_final: 0.8533 (tpt) REVERT: V 480 ARG cc_start: 0.8562 (mmm160) cc_final: 0.8255 (mmm160) REVERT: U 911 ARG cc_start: 0.8227 (mmt-90) cc_final: 0.7919 (mmt-90) REVERT: U 913 ARG cc_start: 0.8128 (ptt90) cc_final: 0.7866 (ptt90) outliers start: 102 outliers final: 67 residues processed: 782 average time/residue: 0.2172 time to fit residues: 249.0968 Evaluate side-chains 794 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 720 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 296 ASN Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 332 LEU Chi-restraints excluded: chain K residue 393 THR Chi-restraints excluded: chain K residue 402 LYS Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 380 ARG Chi-restraints excluded: chain N residue 467 SER Chi-restraints excluded: chain N residue 477 SER Chi-restraints excluded: chain N residue 586 LEU Chi-restraints excluded: chain N residue 607 ARG Chi-restraints excluded: chain N residue 627 GLN Chi-restraints excluded: chain N residue 644 MET Chi-restraints excluded: chain O residue 134 ILE Chi-restraints excluded: chain O residue 348 CYS Chi-restraints excluded: chain O residue 401 GLU Chi-restraints excluded: chain O residue 474 ASP Chi-restraints excluded: chain O residue 619 PHE Chi-restraints excluded: chain O residue 623 VAL Chi-restraints excluded: chain P residue 68 ARG Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 172 LEU Chi-restraints excluded: chain P residue 224 PHE Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain P residue 282 VAL Chi-restraints excluded: chain P residue 299 LEU Chi-restraints excluded: chain P residue 313 THR Chi-restraints excluded: chain P residue 315 GLN Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 364 THR Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain P residue 531 LEU Chi-restraints excluded: chain Q residue 26 TYR Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 182 HIS Chi-restraints excluded: chain Q residue 394 MET Chi-restraints excluded: chain Q residue 470 VAL Chi-restraints excluded: chain R residue 398 CYS Chi-restraints excluded: chain R residue 435 GLU Chi-restraints excluded: chain R residue 463 LEU Chi-restraints excluded: chain R residue 516 MET Chi-restraints excluded: chain R residue 600 VAL Chi-restraints excluded: chain R residue 928 ARG Chi-restraints excluded: chain S residue 102 MET Chi-restraints excluded: chain S residue 321 THR Chi-restraints excluded: chain S residue 336 LEU Chi-restraints excluded: chain S residue 436 THR Chi-restraints excluded: chain S residue 437 LEU Chi-restraints excluded: chain S residue 544 THR Chi-restraints excluded: chain S residue 583 LYS Chi-restraints excluded: chain T residue 349 GLU Chi-restraints excluded: chain T residue 473 GLU Chi-restraints excluded: chain V residue 119 ILE Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 150 GLU Chi-restraints excluded: chain V residue 260 THR Chi-restraints excluded: chain V residue 267 PHE Chi-restraints excluded: chain V residue 276 LEU Chi-restraints excluded: chain V residue 379 VAL Chi-restraints excluded: chain V residue 558 VAL Chi-restraints excluded: chain U residue 845 VAL Chi-restraints excluded: chain U residue 869 ASN Chi-restraints excluded: chain U residue 876 THR Chi-restraints excluded: chain U residue 978 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 95 optimal weight: 0.6980 chunk 292 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 221 optimal weight: 0.0970 chunk 291 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 266 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 338 ASN N 129 ASN N 627 GLN ** Q 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.139872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.117285 restraints weight = 61622.207| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.60 r_work: 0.3392 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26528 Z= 0.140 Angle : 0.657 12.145 35946 Z= 0.327 Chirality : 0.042 0.278 3948 Planarity : 0.005 0.075 4725 Dihedral : 4.321 29.322 3581 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.16 % Allowed : 24.98 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 3185 helix: 1.81 (0.14), residues: 1451 sheet: 0.01 (0.36), residues: 204 loop : -1.30 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 998 TYR 0.022 0.001 TYR K 369 PHE 0.033 0.002 PHE V 75 TRP 0.032 0.001 TRP S 419 HIS 0.004 0.001 HIS P 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (26516) covalent geometry : angle 0.64565 / 0.33 (35928) hydrogen bonds : bond 0.04619 / 3.16 ( 1209) hydrogen bonds : angle 4.40821 / 3.18 ( 3492) metal coordination : bond 0.00535 / 0.21 ( 12) metal coordination : angle 5.43012 / 3.07 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 737 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 324 ARG cc_start: 0.8814 (ttt180) cc_final: 0.8304 (ttt180) REVERT: K 325 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8668 (mtm) REVERT: N 180 ARG cc_start: 0.7451 (mtt180) cc_final: 0.6986 (mtt90) REVERT: N 221 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8414 (m) REVERT: N 331 TYR cc_start: 0.8471 (p90) cc_final: 0.7848 (p90) REVERT: N 569 MET cc_start: 0.7544 (mmm) cc_final: 0.7268 (mmp) REVERT: N 627 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8345 (tp40) REVERT: O 401 GLU cc_start: 0.3187 (OUTLIER) cc_final: -0.1136 (pm20) REVERT: O 405 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7483 (mp10) REVERT: O 424 GLN cc_start: 0.8726 (tp-100) cc_final: 0.8375 (tm-30) REVERT: O 627 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8082 (tm-30) REVERT: P 140 ASP cc_start: 0.6311 (t70) cc_final: 0.6101 (t70) REVERT: P 224 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7873 (m-80) REVERT: P 230 GLU cc_start: 0.7107 (mp0) cc_final: 0.6755 (mp0) REVERT: P 305 GLU cc_start: 0.8687 (tp30) cc_final: 0.8054 (tp30) REVERT: P 452 PHE cc_start: 0.6616 (p90) cc_final: 0.6384 (p90) REVERT: Q 115 ARG cc_start: 0.7424 (mmt90) cc_final: 0.6656 (mmt180) REVERT: Q 145 ASP cc_start: 0.7924 (t0) cc_final: 0.7493 (t0) REVERT: Q 157 GLU cc_start: 0.7987 (mp0) cc_final: 0.7703 (mp0) REVERT: Q 175 GLN cc_start: 0.8549 (pp30) cc_final: 0.8268 (pp30) REVERT: Q 181 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8346 (mm110) REVERT: Q 194 PHE cc_start: 0.7429 (p90) cc_final: 0.6985 (p90) REVERT: Q 397 LYS cc_start: 0.8672 (tppt) cc_final: 0.8386 (tppt) REVERT: R 355 GLU cc_start: 0.8045 (pm20) cc_final: 0.7795 (pm20) REVERT: R 387 GLU cc_start: 0.8034 (tp30) cc_final: 0.7795 (tp30) REVERT: R 388 MET cc_start: 0.8830 (mtp) cc_final: 0.8471 (mmm) REVERT: S 224 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7360 (tm-30) REVERT: S 435 GLU cc_start: 0.8469 (pm20) cc_final: 0.8246 (pm20) REVERT: S 590 MET cc_start: 0.8774 (mmm) cc_final: 0.8419 (mmm) REVERT: T 473 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7828 (tm-30) REVERT: V 69 MET cc_start: 0.8847 (pmm) cc_final: 0.8647 (pmm) REVERT: V 150 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7461 (tp30) REVERT: V 173 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8266 (mm-30) REVERT: V 176 ARG cc_start: 0.8154 (mtm110) cc_final: 0.7813 (mtm110) REVERT: V 471 MET cc_start: 0.8743 (tpt) cc_final: 0.8537 (tpt) REVERT: V 480 ARG cc_start: 0.8582 (mmm160) cc_final: 0.8334 (mmm160) REVERT: U 858 LYS cc_start: 0.9132 (mmmt) cc_final: 0.8927 (mmmt) REVERT: U 906 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8125 (tm-30) outliers start: 115 outliers final: 78 residues processed: 795 average time/residue: 0.2147 time to fit residues: 251.6151 Evaluate side-chains 800 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 714 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 296 ASN Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 325 MET Chi-restraints excluded: chain K residue 332 LEU Chi-restraints excluded: chain K residue 393 THR Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 477 SER Chi-restraints excluded: chain N residue 546 LEU Chi-restraints excluded: chain N residue 563 SER Chi-restraints excluded: chain N residue 586 LEU Chi-restraints excluded: chain N residue 607 ARG Chi-restraints excluded: chain N residue 627 GLN Chi-restraints excluded: chain N residue 636 THR Chi-restraints excluded: chain N residue 644 MET Chi-restraints excluded: chain O residue 134 ILE Chi-restraints excluded: chain O residue 348 CYS Chi-restraints excluded: chain O residue 401 GLU Chi-restraints excluded: chain O residue 404 ASN Chi-restraints excluded: chain O residue 405 GLN Chi-restraints excluded: chain O residue 474 ASP Chi-restraints excluded: chain O residue 623 VAL Chi-restraints excluded: chain P residue 68 ARG Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain P residue 172 LEU Chi-restraints excluded: chain P residue 224 PHE Chi-restraints excluded: chain P residue 282 VAL Chi-restraints excluded: chain P residue 299 LEU Chi-restraints excluded: chain P residue 315 GLN Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 364 THR Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain P residue 531 LEU Chi-restraints excluded: chain Q residue 26 TYR Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 182 HIS Chi-restraints excluded: chain Q residue 394 MET Chi-restraints excluded: chain Q residue 461 GLU Chi-restraints excluded: chain Q residue 470 VAL Chi-restraints excluded: chain R residue 398 CYS Chi-restraints excluded: chain R residue 435 GLU Chi-restraints excluded: chain R residue 463 LEU Chi-restraints excluded: chain R residue 516 MET Chi-restraints excluded: chain R residue 518 THR Chi-restraints excluded: chain R residue 520 GLU Chi-restraints excluded: chain R residue 600 VAL Chi-restraints excluded: chain R residue 907 ASN Chi-restraints excluded: chain R residue 928 ARG Chi-restraints excluded: chain R residue 945 GLU Chi-restraints excluded: chain R residue 999 LEU Chi-restraints excluded: chain S residue 102 MET Chi-restraints excluded: chain S residue 321 THR Chi-restraints excluded: chain S residue 322 LEU Chi-restraints excluded: chain S residue 336 LEU Chi-restraints excluded: chain S residue 436 THR Chi-restraints excluded: chain S residue 437 LEU Chi-restraints excluded: chain S residue 544 THR Chi-restraints excluded: chain S residue 583 LYS Chi-restraints excluded: chain T residue 349 GLU Chi-restraints excluded: chain T residue 473 GLU Chi-restraints excluded: chain V residue 119 ILE Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 150 GLU Chi-restraints excluded: chain V residue 260 THR Chi-restraints excluded: chain V residue 267 PHE Chi-restraints excluded: chain V residue 276 LEU Chi-restraints excluded: chain V residue 379 VAL Chi-restraints excluded: chain V residue 526 GLN Chi-restraints excluded: chain V residue 558 VAL Chi-restraints excluded: chain U residue 845 VAL Chi-restraints excluded: chain U residue 869 ASN Chi-restraints excluded: chain U residue 876 THR Chi-restraints excluded: chain U residue 886 ARG Chi-restraints excluded: chain U residue 978 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 101 optimal weight: 0.8980 chunk 295 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 227 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 226 optimal weight: 0.8980 chunk 271 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 249 optimal weight: 0.7980 chunk 152 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 200 GLN ** K 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 ASN N 215 HIS N 424 GLN ** N 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 521 GLN P 534 GLN Q 11 HIS ** Q 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 147 ASN T 421 ASN V 312 GLN V 521 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.137421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.114705 restraints weight = 61364.384| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.61 r_work: 0.3365 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26528 Z= 0.166 Angle : 0.671 12.037 35946 Z= 0.337 Chirality : 0.043 0.245 3948 Planarity : 0.005 0.076 4725 Dihedral : 4.403 29.470 3581 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.09 % Allowed : 25.74 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.15), residues: 3185 helix: 1.76 (0.14), residues: 1452 sheet: -0.03 (0.36), residues: 204 loop : -1.33 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 445 TYR 0.025 0.001 TYR K 369 PHE 0.037 0.002 PHE V 75 TRP 0.024 0.001 TRP S 419 HIS 0.005 0.001 HIS R 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (26516) covalent geometry : angle 0.65999 / 0.34 (35928) hydrogen bonds : bond 0.04882 / 3.34 ( 1209) hydrogen bonds : angle 4.44106 / 3.22 ( 3492) metal coordination : bond 0.00601 / 0.27 ( 12) metal coordination : angle 5.54900 / 3.15 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 736 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 173 GLN cc_start: 0.8527 (tp-100) cc_final: 0.8286 (tp-100) REVERT: K 323 ASN cc_start: 0.8492 (t0) cc_final: 0.8024 (t0) REVERT: K 324 ARG cc_start: 0.8505 (ttt180) cc_final: 0.8253 (ttt180) REVERT: K 325 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8749 (mtm) REVERT: K 369 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.6929 (m-10) REVERT: N 221 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8450 (m) REVERT: N 331 TYR cc_start: 0.8486 (p90) cc_final: 0.7881 (p90) REVERT: N 369 MET cc_start: 0.7999 (mpp) cc_final: 0.7711 (mpp) REVERT: N 569 MET cc_start: 0.7597 (mmm) cc_final: 0.7361 (mmm) REVERT: N 642 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.5803 (t80) REVERT: O 401 GLU cc_start: 0.3356 (OUTLIER) cc_final: -0.1162 (pm20) REVERT: O 405 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7550 (mp10) REVERT: O 424 GLN cc_start: 0.8747 (tp-100) cc_final: 0.8373 (tm-30) REVERT: O 627 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8044 (tm-30) REVERT: P 224 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: P 230 GLU cc_start: 0.7120 (mp0) cc_final: 0.6763 (mp0) REVERT: P 305 GLU cc_start: 0.8686 (tp30) cc_final: 0.8109 (tp30) REVERT: Q 115 ARG cc_start: 0.7385 (mmt90) cc_final: 0.6814 (mmt180) REVERT: Q 145 ASP cc_start: 0.7945 (t0) cc_final: 0.7448 (t0) REVERT: Q 157 GLU cc_start: 0.7963 (mp0) cc_final: 0.7687 (mp0) REVERT: Q 175 GLN cc_start: 0.8560 (pp30) cc_final: 0.8285 (pp30) REVERT: Q 177 LEU cc_start: 0.8976 (mt) cc_final: 0.8748 (mt) REVERT: Q 181 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8371 (mm110) REVERT: Q 194 PHE cc_start: 0.7621 (p90) cc_final: 0.7125 (p90) REVERT: Q 397 LYS cc_start: 0.8719 (tppt) cc_final: 0.8425 (tppt) REVERT: R 351 LYS cc_start: 0.8585 (mmmt) cc_final: 0.8364 (mttp) REVERT: R 355 GLU cc_start: 0.8049 (pm20) cc_final: 0.7783 (pm20) REVERT: R 387 GLU cc_start: 0.8071 (tp30) cc_final: 0.7819 (tp30) REVERT: S 224 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7436 (tm-30) REVERT: S 435 GLU cc_start: 0.8461 (pm20) cc_final: 0.8227 (pm20) REVERT: S 590 MET cc_start: 0.8797 (mmm) cc_final: 0.8375 (mmm) REVERT: T 395 GLN cc_start: 0.8511 (tt0) cc_final: 0.8256 (tt0) REVERT: T 468 MET cc_start: 0.8758 (mtp) cc_final: 0.8524 (mtt) REVERT: T 473 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: V 69 MET cc_start: 0.8944 (pmm) cc_final: 0.8626 (pmm) REVERT: V 150 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7554 (tp30) REVERT: V 173 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8161 (mm-30) REVERT: V 176 ARG cc_start: 0.8150 (mtm110) cc_final: 0.7945 (mtm110) REVERT: V 480 ARG cc_start: 0.8598 (mmm160) cc_final: 0.8376 (mmm160) REVERT: U 906 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8489 (tm-30) REVERT: U 911 ARG cc_start: 0.8133 (mmt180) cc_final: 0.7651 (mmt180) REVERT: U 913 ARG cc_start: 0.8158 (ptt90) cc_final: 0.7906 (ptt90) outliers start: 113 outliers final: 80 residues processed: 794 average time/residue: 0.2132 time to fit residues: 249.1485 Evaluate side-chains 822 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 733 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 296 ASN Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 325 MET Chi-restraints excluded: chain K residue 332 LEU Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain K residue 369 TYR Chi-restraints excluded: chain K residue 393 THR Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 380 ARG Chi-restraints excluded: chain N residue 477 SER Chi-restraints excluded: chain N residue 563 SER Chi-restraints excluded: chain N residue 586 LEU Chi-restraints excluded: chain N residue 607 ARG Chi-restraints excluded: chain N residue 636 THR Chi-restraints excluded: chain N residue 642 PHE Chi-restraints excluded: chain N residue 644 MET Chi-restraints excluded: chain O residue 134 ILE Chi-restraints excluded: chain O residue 348 CYS Chi-restraints excluded: chain O residue 401 GLU Chi-restraints excluded: chain O residue 404 ASN Chi-restraints excluded: chain O residue 405 GLN Chi-restraints excluded: chain O residue 474 ASP Chi-restraints excluded: chain O residue 623 VAL Chi-restraints excluded: chain P residue 68 ARG Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain P residue 172 LEU Chi-restraints excluded: chain P residue 224 PHE Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain P residue 282 VAL Chi-restraints excluded: chain P residue 299 LEU Chi-restraints excluded: chain P residue 315 GLN Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 364 THR Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 147 ASN Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 182 HIS Chi-restraints excluded: chain Q residue 394 MET Chi-restraints excluded: chain Q residue 470 VAL Chi-restraints excluded: chain R residue 398 CYS Chi-restraints excluded: chain R residue 435 GLU Chi-restraints excluded: chain R residue 463 LEU Chi-restraints excluded: chain R residue 516 MET Chi-restraints excluded: chain R residue 518 THR Chi-restraints excluded: chain R residue 520 GLU Chi-restraints excluded: chain R residue 600 VAL Chi-restraints excluded: chain R residue 618 SER Chi-restraints excluded: chain R residue 907 ASN Chi-restraints excluded: chain R residue 928 ARG Chi-restraints excluded: chain R residue 945 GLU Chi-restraints excluded: chain R residue 999 LEU Chi-restraints excluded: chain S residue 102 MET Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 321 THR Chi-restraints excluded: chain S residue 322 LEU Chi-restraints excluded: chain S residue 336 LEU Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 436 THR Chi-restraints excluded: chain S residue 544 THR Chi-restraints excluded: chain S residue 583 LYS Chi-restraints excluded: chain T residue 349 GLU Chi-restraints excluded: chain T residue 473 GLU Chi-restraints excluded: chain V residue 119 ILE Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 150 GLU Chi-restraints excluded: chain V residue 260 THR Chi-restraints excluded: chain V residue 267 PHE Chi-restraints excluded: chain V residue 276 LEU Chi-restraints excluded: chain V residue 379 VAL Chi-restraints excluded: chain V residue 526 GLN Chi-restraints excluded: chain V residue 558 VAL Chi-restraints excluded: chain U residue 845 VAL Chi-restraints excluded: chain U residue 869 ASN Chi-restraints excluded: chain U residue 876 THR Chi-restraints excluded: chain U residue 886 ARG Chi-restraints excluded: chain U residue 907 LEU Chi-restraints excluded: chain U residue 961 LEU Chi-restraints excluded: chain U residue 978 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 18 optimal weight: 0.0270 chunk 232 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 280 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 205 optimal weight: 0.6980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 ASN ** N 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 419 ASN P 521 GLN ** Q 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 421 ASN V 316 GLN ** U 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.137971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115294 restraints weight = 61722.536| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.60 r_work: 0.3376 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26528 Z= 0.154 Angle : 0.683 13.692 35946 Z= 0.342 Chirality : 0.043 0.244 3948 Planarity : 0.005 0.072 4725 Dihedral : 4.422 29.400 3581 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.87 % Allowed : 26.57 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 3185 helix: 1.72 (0.14), residues: 1456 sheet: -0.02 (0.36), residues: 204 loop : -1.32 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG T 490 TYR 0.026 0.001 TYR K 369 PHE 0.038 0.002 PHE V 75 TRP 0.043 0.002 TRP S 419 HIS 0.005 0.001 HIS R 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (26516) covalent geometry : angle 0.67243 / 0.34 (35928) hydrogen bonds : bond 0.04794 / 3.29 ( 1209) hydrogen bonds : angle 4.42787 / 3.21 ( 3492) metal coordination : bond 0.00534 / 0.23 ( 12) metal coordination : angle 5.41285 / 3.06 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 740 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 173 GLN cc_start: 0.8680 (tp-100) cc_final: 0.8364 (tp-100) REVERT: K 209 ARG cc_start: 0.7569 (ptm-80) cc_final: 0.7357 (ptp90) REVERT: K 323 ASN cc_start: 0.8475 (t0) cc_final: 0.7997 (t0) REVERT: K 324 ARG cc_start: 0.8471 (ttt180) cc_final: 0.8245 (ttt180) REVERT: K 325 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8700 (mtm) REVERT: K 369 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.7008 (m-10) REVERT: N 221 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8436 (m) REVERT: N 331 TYR cc_start: 0.8470 (p90) cc_final: 0.7874 (p90) REVERT: N 369 MET cc_start: 0.8000 (mpp) cc_final: 0.7701 (mpp) REVERT: N 642 PHE cc_start: 0.6873 (OUTLIER) cc_final: 0.5564 (t80) REVERT: O 401 GLU cc_start: 0.3298 (OUTLIER) cc_final: -0.1243 (pm20) REVERT: O 405 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7531 (mp10) REVERT: O 424 GLN cc_start: 0.8768 (tp-100) cc_final: 0.8405 (tm-30) REVERT: O 627 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8112 (tm-30) REVERT: P 224 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.8071 (m-10) REVERT: P 295 GLU cc_start: 0.6313 (pm20) cc_final: 0.6043 (pm20) REVERT: P 305 GLU cc_start: 0.8652 (tp30) cc_final: 0.8080 (tp30) REVERT: P 428 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6606 (pm20) REVERT: Q 29 MET cc_start: 0.7975 (pmm) cc_final: 0.7631 (pmm) REVERT: Q 115 ARG cc_start: 0.7373 (mmt90) cc_final: 0.6781 (mmt180) REVERT: Q 145 ASP cc_start: 0.7910 (t0) cc_final: 0.7506 (t0) REVERT: Q 157 GLU cc_start: 0.7969 (mp0) cc_final: 0.7479 (mp0) REVERT: Q 175 GLN cc_start: 0.8596 (pp30) cc_final: 0.8312 (pp30) REVERT: Q 177 LEU cc_start: 0.8955 (mt) cc_final: 0.8709 (mt) REVERT: Q 181 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8365 (mm110) REVERT: Q 194 PHE cc_start: 0.7527 (p90) cc_final: 0.7066 (p90) REVERT: Q 397 LYS cc_start: 0.8735 (tppt) cc_final: 0.8444 (tppt) REVERT: R 351 LYS cc_start: 0.8587 (mmmt) cc_final: 0.8336 (mttp) REVERT: R 355 GLU cc_start: 0.8011 (pm20) cc_final: 0.7741 (pm20) REVERT: R 388 MET cc_start: 0.8878 (mtp) cc_final: 0.8509 (mmm) REVERT: R 930 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8184 (t) REVERT: S 224 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7405 (tm-30) REVERT: S 435 GLU cc_start: 0.8495 (pm20) cc_final: 0.8269 (pm20) REVERT: S 590 MET cc_start: 0.8805 (mmm) cc_final: 0.8347 (mmm) REVERT: T 395 GLN cc_start: 0.8474 (tt0) cc_final: 0.8212 (tt0) REVERT: T 468 MET cc_start: 0.8624 (mtp) cc_final: 0.8380 (mtt) REVERT: V 69 MET cc_start: 0.8894 (pmm) cc_final: 0.8689 (pmm) REVERT: V 150 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7524 (tp30) REVERT: V 173 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8103 (mm-30) REVERT: V 176 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7871 (mtm110) REVERT: V 471 MET cc_start: 0.8806 (tpt) cc_final: 0.8594 (mmm) REVERT: V 480 ARG cc_start: 0.8564 (mmm160) cc_final: 0.8350 (mmm160) REVERT: U 906 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8355 (tm-30) REVERT: U 911 ARG cc_start: 0.8128 (mmt180) cc_final: 0.7650 (mmt180) REVERT: U 913 ARG cc_start: 0.8146 (ptt90) cc_final: 0.7945 (ptt90) outliers start: 107 outliers final: 81 residues processed: 791 average time/residue: 0.2171 time to fit residues: 252.3919 Evaluate side-chains 803 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 712 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 296 ASN Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 325 MET Chi-restraints excluded: chain K residue 332 LEU Chi-restraints excluded: chain K residue 369 TYR Chi-restraints excluded: chain K residue 393 THR Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 380 ARG Chi-restraints excluded: chain N residue 477 SER Chi-restraints excluded: chain N residue 546 LEU Chi-restraints excluded: chain N residue 563 SER Chi-restraints excluded: chain N residue 586 LEU Chi-restraints excluded: chain N residue 607 ARG Chi-restraints excluded: chain N residue 636 THR Chi-restraints excluded: chain N residue 642 PHE Chi-restraints excluded: chain O residue 134 ILE Chi-restraints excluded: chain O residue 348 CYS Chi-restraints excluded: chain O residue 393 LEU Chi-restraints excluded: chain O residue 401 GLU Chi-restraints excluded: chain O residue 405 GLN Chi-restraints excluded: chain O residue 474 ASP Chi-restraints excluded: chain P residue 68 ARG Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain P residue 172 LEU Chi-restraints excluded: chain P residue 224 PHE Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain P residue 282 VAL Chi-restraints excluded: chain P residue 299 LEU Chi-restraints excluded: chain P residue 309 MET Chi-restraints excluded: chain P residue 315 GLN Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 364 THR Chi-restraints excluded: chain P residue 428 GLU Chi-restraints excluded: chain Q residue 9 ASN Chi-restraints excluded: chain Q residue 26 TYR Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 147 ASN Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 182 HIS Chi-restraints excluded: chain Q residue 394 MET Chi-restraints excluded: chain Q residue 468 THR Chi-restraints excluded: chain Q residue 470 VAL Chi-restraints excluded: chain R residue 398 CYS Chi-restraints excluded: chain R residue 435 GLU Chi-restraints excluded: chain R residue 463 LEU Chi-restraints excluded: chain R residue 516 MET Chi-restraints excluded: chain R residue 518 THR Chi-restraints excluded: chain R residue 520 GLU Chi-restraints excluded: chain R residue 600 VAL Chi-restraints excluded: chain R residue 618 SER Chi-restraints excluded: chain R residue 907 ASN Chi-restraints excluded: chain R residue 928 ARG Chi-restraints excluded: chain R residue 930 VAL Chi-restraints excluded: chain R residue 945 GLU Chi-restraints excluded: chain R residue 999 LEU Chi-restraints excluded: chain S residue 102 MET Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 321 THR Chi-restraints excluded: chain S residue 322 LEU Chi-restraints excluded: chain S residue 336 LEU Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 436 THR Chi-restraints excluded: chain S residue 544 THR Chi-restraints excluded: chain S residue 583 LYS Chi-restraints excluded: chain T residue 349 GLU Chi-restraints excluded: chain T residue 421 ASN Chi-restraints excluded: chain V residue 119 ILE Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 150 GLU Chi-restraints excluded: chain V residue 237 LEU Chi-restraints excluded: chain V residue 260 THR Chi-restraints excluded: chain V residue 267 PHE Chi-restraints excluded: chain V residue 276 LEU Chi-restraints excluded: chain V residue 379 VAL Chi-restraints excluded: chain V residue 526 GLN Chi-restraints excluded: chain V residue 558 VAL Chi-restraints excluded: chain U residue 845 VAL Chi-restraints excluded: chain U residue 869 ASN Chi-restraints excluded: chain U residue 876 THR Chi-restraints excluded: chain U residue 886 ARG Chi-restraints excluded: chain U residue 961 LEU Chi-restraints excluded: chain U residue 978 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 203 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 GLN ** K 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 ASN O 421 GLN ** P 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 521 GLN P 534 GLN ** Q 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 147 ASN T 421 ASN V 312 GLN ** U 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.136679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114153 restraints weight = 61762.910| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.58 r_work: 0.3356 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26528 Z= 0.177 Angle : 0.707 13.527 35946 Z= 0.357 Chirality : 0.044 0.308 3948 Planarity : 0.005 0.074 4725 Dihedral : 4.485 29.595 3581 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.20 % Allowed : 26.83 % Favored : 68.97 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3185 helix: 1.66 (0.14), residues: 1458 sheet: -0.10 (0.36), residues: 204 loop : -1.35 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 998 TYR 0.026 0.002 TYR K 369 PHE 0.036 0.002 PHE V 75 TRP 0.035 0.002 TRP S 419 HIS 0.005 0.001 HIS P 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (26516) covalent geometry : angle 0.69636 / 0.36 (35928) hydrogen bonds : bond 0.05042 / 3.45 ( 1209) hydrogen bonds : angle 4.46566 / 3.25 ( 3492) metal coordination : bond 0.00620 / 0.29 ( 12) metal coordination : angle 5.57887 / 3.17 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 732 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 173 GLN cc_start: 0.8657 (tp-100) cc_final: 0.8329 (tp-100) REVERT: K 317 ARG cc_start: 0.9193 (mmm-85) cc_final: 0.8813 (tpp80) REVERT: K 323 ASN cc_start: 0.8513 (t0) cc_final: 0.8018 (t0) REVERT: K 324 ARG cc_start: 0.8486 (ttt180) cc_final: 0.8249 (ttt180) REVERT: K 325 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8637 (mtm) REVERT: K 369 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.7123 (m-10) REVERT: N 221 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8456 (m) REVERT: N 331 TYR cc_start: 0.8487 (p90) cc_final: 0.7914 (p90) REVERT: N 369 MET cc_start: 0.8001 (mpp) cc_final: 0.7705 (mpp) REVERT: N 642 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.5749 (t80) REVERT: O 398 ARG cc_start: 0.8969 (tpt-90) cc_final: 0.8720 (tpt-90) REVERT: O 401 GLU cc_start: 0.3391 (OUTLIER) cc_final: -0.1222 (pm20) REVERT: O 405 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7630 (mp10) REVERT: O 424 GLN cc_start: 0.8776 (tp-100) cc_final: 0.8428 (tm-30) REVERT: O 627 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8156 (tm-30) REVERT: P 68 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6157 (ttt-90) REVERT: P 224 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.8077 (m-10) REVERT: P 295 GLU cc_start: 0.6470 (pm20) cc_final: 0.6167 (pm20) REVERT: P 305 GLU cc_start: 0.8668 (tp30) cc_final: 0.8101 (tp30) REVERT: Q 33 GLU cc_start: 0.7715 (pm20) cc_final: 0.7478 (pm20) REVERT: Q 115 ARG cc_start: 0.7363 (mmt90) cc_final: 0.6756 (mmt180) REVERT: Q 145 ASP cc_start: 0.7943 (t0) cc_final: 0.7426 (t0) REVERT: Q 157 GLU cc_start: 0.7967 (mp0) cc_final: 0.7402 (mp0) REVERT: Q 175 GLN cc_start: 0.8592 (pp30) cc_final: 0.8309 (pp30) REVERT: Q 177 LEU cc_start: 0.8970 (mt) cc_final: 0.8726 (mt) REVERT: Q 181 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8378 (mm110) REVERT: Q 194 PHE cc_start: 0.7577 (p90) cc_final: 0.7057 (p90) REVERT: Q 397 LYS cc_start: 0.8764 (tppt) cc_final: 0.8478 (tppt) REVERT: R 351 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8370 (mttp) REVERT: R 355 GLU cc_start: 0.8003 (pm20) cc_final: 0.7743 (pm20) REVERT: R 388 MET cc_start: 0.8901 (mtp) cc_final: 0.8535 (mmm) REVERT: S 224 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7451 (tm-30) REVERT: S 435 GLU cc_start: 0.8497 (pm20) cc_final: 0.8271 (pm20) REVERT: S 590 MET cc_start: 0.8821 (mmm) cc_final: 0.8325 (mmm) REVERT: T 395 GLN cc_start: 0.8479 (tt0) cc_final: 0.8215 (tt0) REVERT: V 150 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7486 (tp30) REVERT: V 173 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8101 (mm-30) REVERT: V 176 ARG cc_start: 0.8102 (mtm110) cc_final: 0.7876 (mtm110) REVERT: V 471 MET cc_start: 0.8809 (tpt) cc_final: 0.8605 (mmm) REVERT: V 480 ARG cc_start: 0.8596 (mmm160) cc_final: 0.8363 (mmm160) REVERT: U 906 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8370 (tm-30) REVERT: U 911 ARG cc_start: 0.8260 (mmt180) cc_final: 0.7670 (mmt180) outliers start: 116 outliers final: 90 residues processed: 787 average time/residue: 0.2160 time to fit residues: 249.7493 Evaluate side-chains 821 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 722 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 296 ASN Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 325 MET Chi-restraints excluded: chain K residue 332 LEU Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain K residue 369 TYR Chi-restraints excluded: chain K residue 393 THR Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 333 HIS Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 380 ARG Chi-restraints excluded: chain N residue 477 SER Chi-restraints excluded: chain N residue 546 LEU Chi-restraints excluded: chain N residue 563 SER Chi-restraints excluded: chain N residue 586 LEU Chi-restraints excluded: chain N residue 607 ARG Chi-restraints excluded: chain N residue 636 THR Chi-restraints excluded: chain N residue 642 PHE Chi-restraints excluded: chain O residue 134 ILE Chi-restraints excluded: chain O residue 137 LYS Chi-restraints excluded: chain O residue 348 CYS Chi-restraints excluded: chain O residue 401 GLU Chi-restraints excluded: chain O residue 404 ASN Chi-restraints excluded: chain O residue 405 GLN Chi-restraints excluded: chain O residue 474 ASP Chi-restraints excluded: chain P residue 68 ARG Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain P residue 172 LEU Chi-restraints excluded: chain P residue 224 PHE Chi-restraints excluded: chain P residue 227 LEU Chi-restraints excluded: chain P residue 282 VAL Chi-restraints excluded: chain P residue 299 LEU Chi-restraints excluded: chain P residue 309 MET Chi-restraints excluded: chain P residue 315 GLN Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 364 THR Chi-restraints excluded: chain P residue 453 LEU Chi-restraints excluded: chain Q residue 9 ASN Chi-restraints excluded: chain Q residue 26 TYR Chi-restraints excluded: chain Q residue 31 ARG Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 147 ASN Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 182 HIS Chi-restraints excluded: chain Q residue 394 MET Chi-restraints excluded: chain Q residue 468 THR Chi-restraints excluded: chain Q residue 470 VAL Chi-restraints excluded: chain R residue 398 CYS Chi-restraints excluded: chain R residue 435 GLU Chi-restraints excluded: chain R residue 463 LEU Chi-restraints excluded: chain R residue 516 MET Chi-restraints excluded: chain R residue 518 THR Chi-restraints excluded: chain R residue 520 GLU Chi-restraints excluded: chain R residue 600 VAL Chi-restraints excluded: chain R residue 618 SER Chi-restraints excluded: chain R residue 907 ASN Chi-restraints excluded: chain R residue 928 ARG Chi-restraints excluded: chain R residue 945 GLU Chi-restraints excluded: chain R residue 999 LEU Chi-restraints excluded: chain S residue 102 MET Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 321 THR Chi-restraints excluded: chain S residue 322 LEU Chi-restraints excluded: chain S residue 336 LEU Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 436 THR Chi-restraints excluded: chain S residue 544 THR Chi-restraints excluded: chain S residue 583 LYS Chi-restraints excluded: chain T residue 349 GLU Chi-restraints excluded: chain T residue 421 ASN Chi-restraints excluded: chain V residue 119 ILE Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 150 GLU Chi-restraints excluded: chain V residue 237 LEU Chi-restraints excluded: chain V residue 243 VAL Chi-restraints excluded: chain V residue 260 THR Chi-restraints excluded: chain V residue 267 PHE Chi-restraints excluded: chain V residue 276 LEU Chi-restraints excluded: chain V residue 379 VAL Chi-restraints excluded: chain V residue 526 GLN Chi-restraints excluded: chain V residue 558 VAL Chi-restraints excluded: chain U residue 845 VAL Chi-restraints excluded: chain U residue 869 ASN Chi-restraints excluded: chain U residue 876 THR Chi-restraints excluded: chain U residue 886 ARG Chi-restraints excluded: chain U residue 907 LEU Chi-restraints excluded: chain U residue 961 LEU Chi-restraints excluded: chain U residue 978 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 205 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 108 optimal weight: 0.0000 chunk 182 optimal weight: 0.0980 chunk 46 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 ASN ** P 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 521 GLN ** Q 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 147 ASN ** R 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 594 ASN T 345 ASN T 368 ASN T 421 ASN V 312 GLN V 316 GLN ** U 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.138811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.116297 restraints weight = 61645.139| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.61 r_work: 0.3380 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26528 Z= 0.144 Angle : 0.714 14.431 35946 Z= 0.359 Chirality : 0.043 0.262 3948 Planarity : 0.005 0.078 4725 Dihedral : 4.459 29.201 3581 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.84 % Allowed : 27.08 % Favored : 69.08 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3185 helix: 1.69 (0.14), residues: 1458 sheet: -0.11 (0.36), residues: 204 loop : -1.34 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 998 TYR 0.036 0.001 TYR Q 153 PHE 0.049 0.002 PHE Q 128 TRP 0.032 0.001 TRP S 419 HIS 0.004 0.001 HIS P 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (26516) covalent geometry : angle 0.70440 / 0.36 (35928) hydrogen bonds : bond 0.04742 / 3.26 ( 1209) hydrogen bonds : angle 4.42319 / 3.22 ( 3492) metal coordination : bond 0.00474 / 0.20 ( 12) metal coordination : angle 5.30195 / 3.01 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 720 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 173 GLN cc_start: 0.8670 (tp-100) cc_final: 0.8363 (tp-100) REVERT: K 317 ARG cc_start: 0.9191 (mmm-85) cc_final: 0.8802 (tpp80) REVERT: K 323 ASN cc_start: 0.8487 (t0) cc_final: 0.7988 (t0) REVERT: K 369 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.7348 (m-10) REVERT: N 221 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8402 (m) REVERT: N 331 TYR cc_start: 0.8501 (p90) cc_final: 0.7905 (p90) REVERT: N 369 MET cc_start: 0.8025 (mpp) cc_final: 0.7716 (mpp) REVERT: N 642 PHE cc_start: 0.6847 (OUTLIER) cc_final: 0.5716 (t80) REVERT: O 401 GLU cc_start: 0.3298 (OUTLIER) cc_final: -0.1009 (pm20) REVERT: O 405 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7676 (mp10) REVERT: O 424 GLN cc_start: 0.8782 (tp-100) cc_final: 0.8429 (tm-30) REVERT: O 627 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8137 (tm-30) REVERT: P 68 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.6092 (ttt-90) REVERT: P 224 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.8060 (m-10) REVERT: P 295 GLU cc_start: 0.6479 (pm20) cc_final: 0.6179 (pm20) REVERT: P 305 GLU cc_start: 0.8659 (tp30) cc_final: 0.8117 (tp30) REVERT: P 316 GLU cc_start: 0.7895 (tp30) cc_final: 0.7632 (tt0) REVERT: P 452 PHE cc_start: 0.6805 (p90) cc_final: 0.6521 (p90) REVERT: P 456 MET cc_start: 0.7750 (tpt) cc_final: 0.7157 (tpt) REVERT: Q 84 ASP cc_start: 0.5798 (OUTLIER) cc_final: 0.5466 (p0) REVERT: Q 86 TYR cc_start: 0.5510 (m-10) cc_final: 0.4792 (m-10) REVERT: Q 115 ARG cc_start: 0.7669 (mmt90) cc_final: 0.7034 (mmt180) REVERT: Q 145 ASP cc_start: 0.8120 (t0) cc_final: 0.7609 (t0) REVERT: Q 157 GLU cc_start: 0.7963 (mp0) cc_final: 0.7434 (mp0) REVERT: Q 175 GLN cc_start: 0.8624 (pp30) cc_final: 0.8321 (pp30) REVERT: Q 177 LEU cc_start: 0.8979 (mt) cc_final: 0.8720 (mt) REVERT: Q 181 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8364 (mm110) REVERT: Q 194 PHE cc_start: 0.7569 (p90) cc_final: 0.7107 (p90) REVERT: Q 397 LYS cc_start: 0.8695 (tppt) cc_final: 0.8408 (tppt) REVERT: Q 460 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7959 (mm-30) REVERT: R 351 LYS cc_start: 0.8632 (mmmt) cc_final: 0.8377 (mttp) REVERT: R 355 GLU cc_start: 0.7969 (pm20) cc_final: 0.7702 (pm20) REVERT: R 388 MET cc_start: 0.8900 (mtp) cc_final: 0.8538 (mmm) REVERT: R 930 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8018 (t) REVERT: S 224 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7405 (tm-30) REVERT: S 435 GLU cc_start: 0.8528 (pm20) cc_final: 0.8279 (pm20) REVERT: S 590 MET cc_start: 0.8821 (mmm) cc_final: 0.8314 (mmm) REVERT: T 395 GLN cc_start: 0.8443 (tt0) cc_final: 0.8197 (tt0) REVERT: T 397 ASN cc_start: 0.8480 (p0) cc_final: 0.8125 (p0) REVERT: V 69 MET cc_start: 0.8964 (pmm) cc_final: 0.8617 (mpp) REVERT: V 150 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7438 (tp30) REVERT: V 173 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8059 (mm-30) REVERT: V 176 ARG cc_start: 0.8081 (mtm110) cc_final: 0.7834 (mtm110) REVERT: V 471 MET cc_start: 0.8832 (tpt) cc_final: 0.8614 (mmm) REVERT: V 480 ARG cc_start: 0.8616 (mmm160) cc_final: 0.8344 (mmm160) REVERT: U 911 ARG cc_start: 0.8225 (mmt180) cc_final: 0.7696 (mmt180) outliers start: 106 outliers final: 84 residues processed: 775 average time/residue: 0.2125 time to fit residues: 241.9057 Evaluate side-chains 805 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 711 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 296 ASN Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 320 ILE Chi-restraints excluded: chain K residue 325 MET Chi-restraints excluded: chain K residue 332 LEU Chi-restraints excluded: chain K residue 369 TYR Chi-restraints excluded: chain K residue 393 THR Chi-restraints excluded: chain N residue 221 THR Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 380 ARG Chi-restraints excluded: chain N residue 477 SER Chi-restraints excluded: chain N residue 546 LEU Chi-restraints excluded: chain N residue 586 LEU Chi-restraints excluded: chain N residue 607 ARG Chi-restraints excluded: chain N residue 636 THR Chi-restraints excluded: chain N residue 642 PHE Chi-restraints excluded: chain O residue 134 ILE Chi-restraints excluded: chain O residue 320 CYS Chi-restraints excluded: chain O residue 348 CYS Chi-restraints excluded: chain O residue 401 GLU Chi-restraints excluded: chain O residue 404 ASN Chi-restraints excluded: chain O residue 405 GLN Chi-restraints excluded: chain O residue 406 ILE Chi-restraints excluded: chain O residue 474 ASP Chi-restraints excluded: chain O residue 623 VAL Chi-restraints excluded: chain P residue 68 ARG Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain P residue 172 LEU Chi-restraints excluded: chain P residue 224 PHE Chi-restraints excluded: chain P residue 227 LEU Chi-restraints excluded: chain P residue 282 VAL Chi-restraints excluded: chain P residue 299 LEU Chi-restraints excluded: chain P residue 309 MET Chi-restraints excluded: chain P residue 315 GLN Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain P residue 348 ILE Chi-restraints excluded: chain P residue 364 THR Chi-restraints excluded: chain Q residue 9 ASN Chi-restraints excluded: chain Q residue 26 TYR Chi-restraints excluded: chain Q residue 31 ARG Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 58 TYR Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 182 HIS Chi-restraints excluded: chain Q residue 468 THR Chi-restraints excluded: chain Q residue 470 VAL Chi-restraints excluded: chain R residue 398 CYS Chi-restraints excluded: chain R residue 435 GLU Chi-restraints excluded: chain R residue 463 LEU Chi-restraints excluded: chain R residue 516 MET Chi-restraints excluded: chain R residue 518 THR Chi-restraints excluded: chain R residue 520 GLU Chi-restraints excluded: chain R residue 600 VAL Chi-restraints excluded: chain R residue 928 ARG Chi-restraints excluded: chain R residue 930 VAL Chi-restraints excluded: chain R residue 945 GLU Chi-restraints excluded: chain R residue 999 LEU Chi-restraints excluded: chain S residue 102 MET Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 321 THR Chi-restraints excluded: chain S residue 322 LEU Chi-restraints excluded: chain S residue 336 LEU Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 436 THR Chi-restraints excluded: chain S residue 583 LYS Chi-restraints excluded: chain T residue 349 GLU Chi-restraints excluded: chain T residue 368 ASN Chi-restraints excluded: chain T residue 421 ASN Chi-restraints excluded: chain V residue 119 ILE Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 150 GLU Chi-restraints excluded: chain V residue 243 VAL Chi-restraints excluded: chain V residue 260 THR Chi-restraints excluded: chain V residue 267 PHE Chi-restraints excluded: chain V residue 276 LEU Chi-restraints excluded: chain V residue 379 VAL Chi-restraints excluded: chain V residue 526 GLN Chi-restraints excluded: chain V residue 558 VAL Chi-restraints excluded: chain U residue 845 VAL Chi-restraints excluded: chain U residue 869 ASN Chi-restraints excluded: chain U residue 876 THR Chi-restraints excluded: chain U residue 886 ARG Chi-restraints excluded: chain U residue 907 LEU Chi-restraints excluded: chain U residue 961 LEU Chi-restraints excluded: chain U residue 978 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 31 optimal weight: 2.9990 chunk 226 optimal weight: 0.3980 chunk 187 optimal weight: 0.0070 chunk 143 optimal weight: 0.0030 chunk 126 optimal weight: 0.5980 chunk 158 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 281 optimal weight: 0.0970 chunk 44 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 overall best weight: 0.2206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 ASN P 386 HIS P 534 GLN ** Q 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 348 HIS T 368 ASN T 421 ASN ** V 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.140492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.118014 restraints weight = 61601.532| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.61 r_work: 0.3405 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26528 Z= 0.144 Angle : 0.748 19.994 35946 Z= 0.374 Chirality : 0.043 0.323 3948 Planarity : 0.006 0.116 4725 Dihedral : 4.439 28.703 3581 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.22 % Allowed : 27.88 % Favored : 68.90 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 3185 helix: 1.64 (0.14), residues: 1467 sheet: 0.09 (0.36), residues: 198 loop : -1.31 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG U 924 TYR 0.034 0.001 TYR Q 86 PHE 0.042 0.002 PHE V 75 TRP 0.029 0.001 TRP S 419 HIS 0.006 0.001 HIS U 896 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (26516) covalent geometry : angle 0.73910 / 0.37 (35928) hydrogen bonds : bond 0.04523 / 3.10 ( 1209) hydrogen bonds : angle 4.41931 / 3.21 ( 3492) metal coordination : bond 0.00416 / 0.16 ( 12) metal coordination : angle 5.05238 / 2.85 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6370 Ramachandran restraints generated. 3185 Oldfield, 0 Emsley, 3185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 728 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 173 GLN cc_start: 0.8742 (tp-100) cc_final: 0.8424 (tp-100) REVERT: K 317 ARG cc_start: 0.9182 (mmm-85) cc_final: 0.8777 (tpp80) REVERT: K 323 ASN cc_start: 0.8446 (t0) cc_final: 0.7963 (t0) REVERT: K 369 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.7215 (m-10) REVERT: N 331 TYR cc_start: 0.8476 (p90) cc_final: 0.7873 (p90) REVERT: N 369 MET cc_start: 0.8071 (mpp) cc_final: 0.7795 (mpp) REVERT: N 627 GLN cc_start: 0.8671 (tt0) cc_final: 0.8289 (tp-100) REVERT: N 642 PHE cc_start: 0.6696 (OUTLIER) cc_final: 0.5593 (t80) REVERT: O 396 LEU cc_start: 0.9002 (mt) cc_final: 0.8627 (mt) REVERT: O 401 GLU cc_start: 0.3119 (OUTLIER) cc_final: -0.1036 (pm20) REVERT: O 405 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7645 (mp10) REVERT: O 424 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8398 (tm-30) REVERT: O 627 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8125 (tm-30) REVERT: P 68 ARG cc_start: 0.6585 (OUTLIER) cc_final: 0.6032 (ttt-90) REVERT: P 295 GLU cc_start: 0.6468 (pm20) cc_final: 0.6153 (pm20) REVERT: P 305 GLU cc_start: 0.8692 (tp30) cc_final: 0.8119 (tp30) REVERT: P 316 GLU cc_start: 0.7901 (tp30) cc_final: 0.7631 (tt0) REVERT: P 456 MET cc_start: 0.7713 (tpt) cc_final: 0.7129 (tpt) REVERT: Q 145 ASP cc_start: 0.7930 (t0) cc_final: 0.7333 (t0) REVERT: Q 157 GLU cc_start: 0.7985 (mp0) cc_final: 0.7457 (mp0) REVERT: Q 175 GLN cc_start: 0.8597 (pp30) cc_final: 0.8286 (pp30) REVERT: Q 177 LEU cc_start: 0.8983 (mt) cc_final: 0.8715 (mt) REVERT: Q 181 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8363 (mm110) REVERT: Q 194 PHE cc_start: 0.7534 (p90) cc_final: 0.7229 (p90) REVERT: Q 397 LYS cc_start: 0.8672 (tppt) cc_final: 0.8383 (tppt) REVERT: Q 460 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7730 (tp30) REVERT: R 351 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8319 (mttp) REVERT: R 355 GLU cc_start: 0.7962 (pm20) cc_final: 0.7687 (pm20) REVERT: R 388 MET cc_start: 0.8884 (mtp) cc_final: 0.8525 (mmm) REVERT: R 930 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8025 (t) REVERT: S 224 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7291 (tm-30) REVERT: S 435 GLU cc_start: 0.8495 (pm20) cc_final: 0.8263 (pm20) REVERT: S 590 MET cc_start: 0.8814 (mmm) cc_final: 0.8313 (mmm) REVERT: T 395 GLN cc_start: 0.8426 (tt0) cc_final: 0.8184 (tt0) REVERT: T 397 ASN cc_start: 0.8444 (p0) cc_final: 0.8108 (p0) REVERT: T 523 MET cc_start: 0.7385 (mpp) cc_final: 0.6741 (mtm) REVERT: V 69 MET cc_start: 0.8928 (pmm) cc_final: 0.8615 (mpp) REVERT: V 150 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7371 (tp30) REVERT: V 173 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8059 (mm-30) REVERT: V 176 ARG cc_start: 0.8095 (mtm110) cc_final: 0.7861 (mtm110) REVERT: V 471 MET cc_start: 0.8786 (tpt) cc_final: 0.8567 (mmm) REVERT: V 480 ARG cc_start: 0.8611 (mmm160) cc_final: 0.8370 (mmm160) REVERT: U 891 TYR cc_start: 0.6661 (t80) cc_final: 0.6456 (t80) REVERT: U 906 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8431 (tm-30) REVERT: U 911 ARG cc_start: 0.8135 (mmt180) cc_final: 0.7660 (mmt180) REVERT: U 913 ARG cc_start: 0.8282 (ptt90) cc_final: 0.8079 (ptt90) outliers start: 89 outliers final: 69 residues processed: 770 average time/residue: 0.2127 time to fit residues: 239.8418 Evaluate side-chains 781 residues out of total 2827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 705 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 296 ASN Chi-restraints excluded: chain K residue 300 VAL Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 320 ILE Chi-restraints excluded: chain K residue 325 MET Chi-restraints excluded: chain K residue 332 LEU Chi-restraints excluded: chain K residue 369 TYR Chi-restraints excluded: chain K residue 393 THR Chi-restraints excluded: chain N residue 367 THR Chi-restraints excluded: chain N residue 380 ARG Chi-restraints excluded: chain N residue 477 SER Chi-restraints excluded: chain N residue 546 LEU Chi-restraints excluded: chain N residue 607 ARG Chi-restraints excluded: chain N residue 642 PHE Chi-restraints excluded: chain O residue 134 ILE Chi-restraints excluded: chain O residue 320 CYS Chi-restraints excluded: chain O residue 348 CYS Chi-restraints excluded: chain O residue 401 GLU Chi-restraints excluded: chain O residue 404 ASN Chi-restraints excluded: chain O residue 405 GLN Chi-restraints excluded: chain O residue 406 ILE Chi-restraints excluded: chain O residue 474 ASP Chi-restraints excluded: chain P residue 68 ARG Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain P residue 172 LEU Chi-restraints excluded: chain P residue 227 LEU Chi-restraints excluded: chain P residue 282 VAL Chi-restraints excluded: chain P residue 299 LEU Chi-restraints excluded: chain P residue 309 MET Chi-restraints excluded: chain P residue 315 GLN Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain P residue 364 THR Chi-restraints excluded: chain Q residue 26 TYR Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 58 TYR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 182 HIS Chi-restraints excluded: chain Q residue 468 THR Chi-restraints excluded: chain Q residue 470 VAL Chi-restraints excluded: chain R residue 398 CYS Chi-restraints excluded: chain R residue 435 GLU Chi-restraints excluded: chain R residue 463 LEU Chi-restraints excluded: chain R residue 518 THR Chi-restraints excluded: chain R residue 520 GLU Chi-restraints excluded: chain R residue 600 VAL Chi-restraints excluded: chain R residue 928 ARG Chi-restraints excluded: chain R residue 930 VAL Chi-restraints excluded: chain R residue 999 LEU Chi-restraints excluded: chain S residue 102 MET Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 321 THR Chi-restraints excluded: chain S residue 322 LEU Chi-restraints excluded: chain S residue 436 THR Chi-restraints excluded: chain S residue 583 LYS Chi-restraints excluded: chain T residue 349 GLU Chi-restraints excluded: chain T residue 368 ASN Chi-restraints excluded: chain T residue 421 ASN Chi-restraints excluded: chain V residue 119 ILE Chi-restraints excluded: chain V residue 149 LEU Chi-restraints excluded: chain V residue 150 GLU Chi-restraints excluded: chain V residue 243 VAL Chi-restraints excluded: chain V residue 267 PHE Chi-restraints excluded: chain V residue 276 LEU Chi-restraints excluded: chain V residue 379 VAL Chi-restraints excluded: chain V residue 526 GLN Chi-restraints excluded: chain V residue 558 VAL Chi-restraints excluded: chain U residue 845 VAL Chi-restraints excluded: chain U residue 869 ASN Chi-restraints excluded: chain U residue 886 ARG Chi-restraints excluded: chain U residue 924 ARG Chi-restraints excluded: chain U residue 978 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 35 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 314 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 231 optimal weight: 1.9990 chunk 316 optimal weight: 0.0270 chunk 206 optimal weight: 0.8980 chunk 209 optimal weight: 0.5980 chunk 310 optimal weight: 4.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 ASN N 424 GLN O 333 HIS P 283 ASN P 534 GLN ** Q 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 376 HIS T 421 ASN ** V 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.135625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.111762 restraints weight = 59035.762| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.61 r_work: 0.3395 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26528 Z= 0.148 Angle : 0.746 15.510 35946 Z= 0.375 Chirality : 0.044 0.349 3948 Planarity : 0.006 0.156 4725 Dihedral : 4.468 28.466 3581 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.11 % Allowed : 27.88 % Favored : 69.01 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3185 helix: 1.60 (0.14), residues: 1463 sheet: 0.03 (0.36), residues: 198 loop : -1.31 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG R 998 TYR 0.036 0.001 TYR V 181 PHE 0.052 0.002 PHE Q 128 TRP 0.030 0.001 TRP S 419 HIS 0.008 0.001 HIS O 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (26516) covalent geometry : angle 0.73774 / 0.37 (35928) hydrogen bonds : bond 0.04616 / 3.17 ( 1209) hydrogen bonds : angle 4.44744 / 3.23 ( 3492) metal coordination : bond 0.00454 / 0.19 ( 12) metal coordination : angle 5.13897 / 2.88 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8130.43 seconds wall clock time: 139 minutes 23.59 seconds (8363.59 seconds total)